Detection of nucleic acids from whole

ABSTRACT

Methods of detecting one or more nucleic acids from whole blood or plasma are provided. The nucleic acids are captured on a solid support and detected. Compositions, kits, and systems related to the methods are also described.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a non-provisional utility patent application claiming priority to and benefit of the following prior provisional patent application: U.S. Ser. No. 60/724,205, filed Oct. 5, 2005, entitled “DETECTION OF NUCLEIC ACIDS FROM WHOLE BLOOD” by Zhi Zheng et al., which is incorporated herein by reference in its entirety for all purposes.

FIELD OF THE INVENTION

The present invention is in the field of nucleic acid detection. The invention includes methods for detecting one or more nucleic acids from whole blood, peripheral blood cells, or plasma. The invention also includes compositions and kits related to the methods.

BACKGROUND OF THE INVENTION

Samples of peripheral whole blood are easily obtained from any of a wide variety of organisms, and thus blood would seem to be a rich source of material for gene expression studies. However, the composition of blood presents unusual challenges to the detection of nucleic acids from whole blood samples.

For example, whole blood includes a number of different cell types, including red blood cells (erythrocytes), platelets, and white blood cells (leukocytes). The white blood cells themselves include a variety of cell types, for example, granulocytes, such as neutrophils, basophils, and eosinophils, and mononuclear cells, such as monocytes and lymphocytes (including, e.g., T lymphocytes, B lymphocytes, and natural killer cells). Furthermore, when considering gene expression, only particular forms of particular white blood cell types may be of interest: e.g., active granular natural killer cells, Th-lymphocytes, or activated neutrophils, eosinophils, or basophils, to name only a few of the possible examples. Considering that red blood cells are estimated to occupy about 40-45% of the total blood volume while white blood cells and platelets together occupy only about 1-2% of the total blood volume, the difficulty of detecting a nucleic acid that is expressed only in white blood cells, or only in a particular subset or type of white blood cells, becomes clear.

Detection of nucleic acids from whole blood is further complicated, for example, by the high concentration of protein in blood (e.g., of hemoglobin from the red blood cells and of plasma proteins such as albumin, fibrinogen, and globulins) and by the prevalence of certain nucleic acids, particularly globin mRNA.

Current methods for analysis of gene expression in blood involve isolation of a particular type or group of cells (e.g., by red blood cell lysis, or by centrifugation to obtain peripheral blood mononuclear cells (PBMC)), purification of RNA from blood cells, and/or enzymatic manipulation (e.g., reverse transcription and/or target amplification) of the nucleic acids to be detected.

Among other aspects, the present invention provides methods for nucleic acid detection from whole blood that overcome the above noted difficulties. A complete understanding of the invention will be obtained upon review of the following.

SUMMARY OF THE INVENTION

In one aspect, the invention provides methods of detecting nucleic acids from whole blood. In another aspect, the invention provides methods of detecting nucleic acids from plasma. Compositions related to the methods (e.g., compositions useful in practicing the methods or formed while practicing the methods) are also provided, as are kits for detecting nucleic acids from whole blood or plasma.

A first general class of embodiments provides methods of detecting at least a first target nucleic acid. In the methods, a sample comprising whole blood is provided. The whole blood includes peripheral blood cells, which are lysed to produce a lysate comprising the first target nucleic acid. The first target nucleic acid is contacted with a first set of n capture extenders, wherein n is at least two; this first set of capture extenders is capable of hybridizing to the first target nucleic acid. The first target nucleic acid can be contacted with the first set of capture extenders by, for example, contacting the lysate with the first set of capture extenders. The first target nucleic acid is hybridized to the first set of capture extenders, and the first set of capture extenders is associated with a solid support. The first target nucleic acid is captured on the solid support by hybridizing the first target nucleic acid to the first set of capture extenders and associating the first set of capture extenders with the solid support, and the presence of the first target nucleic acid on the solid support is then detected. The hybridization and association steps can, e.g., be either simultaneous or sequential.

In one class of embodiments, the peripheral blood cells are lysed in the whole blood to produce a whole blood lysate that includes the first target nucleic acid. In this class of embodiments, contacting the first target nucleic acid with the first set of capture extenders typically comprises contacting the whole blood lysate with the first set of capture extenders. In one class of embodiments, the whole blood is applied to a matrix to produce a blood spot, and the blood spot is dried to produce a dried blood spot. The dried blood spot is contacted with an aqueous solution to produce the lysate. In one class of embodiments, the methods include contacting the peripheral blood cells and/or the lysate with an exogenously supplied protease, typically prior to contacting the first target nucleic acid with the first set of capture extenders.

The methods can be applied to detection of essentially any type of nucleic acids. For example, the first target nucleic acid can be a DNA or an RNA. In one class of embodiments, the peripheral blood cells include white blood cells, one or more of which white blood cells comprises the first target nucleic acid.

As noted, the first set of capture extenders includes n capture extenders, where n is at least two. Preferably, n is at least three, and n can be at least four or at least five or more. Typically, but not necessarily, n is at most ten. The capture extenders are optionally bound to the solid support, e.g., covalently or noncovalently, directly or through a linker. In one aspect, the capture extenders are associated with the solid support by hybridization of the capture extenders to one or more capture probes. Thus, in one class of embodiments, a first capture probe is bound to the solid support, and the first set of capture extenders is associated with the solid support by hybridizing the capture extenders to the first capture probe.

The solid support can be essentially any suitable support, including any of a variety of materials, configurations, and the like. For example, in one class of embodiments, the solid support is a substantially planar solid support. In another class of embodiments, the solid support comprises a plurality of particles, e.g., microspheres.

The methods can be conveniently multiplexed to detect two or more target nucleic acids simultaneously. Thus, in one class of embodiments, the lysate comprises a second target nucleic acid and the methods include contacting the second target nucleic acid with a second set of m capture extenders, wherein m is at least two; this second set of capture extenders is capable of hybridizing to the second target nucleic acid. The second target nucleic acid is hybridized to the second set of capture extenders, and the second set of capture extenders is associated with the solid support. Hybridizing the second target nucleic acid to the second set of capture extenders and associating the second set of capture extenders with the solid support captures the second target nucleic acid on the solid support. The presence of the second target nucleic acid on the solid support is then detected. It will be evident that n, the number of capture extenders in the first set, can but need not be the same as m, the number of capture extenders in the second set. As for the first target nucleic acid, the second target nucleic acid can be essentially any type of nucleic acid. It will be evident that third, fourth, fifth, etc. target nucleic acids are optionally also detected.

In one class of embodiments, the solid support is a substantially planar solid support, the first target nucleic acid is captured at a first selected position on the solid support, and the second target nucleic acid is captured at a second selected position on the solid support. For example, the first set of capture extenders can be hybridized to a first capture probe predisposed at the first selected position, while the second set of capture extenders is hybridized to a second capture probe predisposed at the second selected position.

In another class of embodiments, the solid support comprises a population of particles. The population includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first target nucleic acid is captured on a first set of the particles, and the second target nucleic acid is captured on a second set of the particles. For example, the first set of particles can comprise a first capture probe that is capable of hybridizing to the capture extenders comprising the first set of capture extenders (and thereby capturing the first target nucleic acid on the first set of particles), and the second set of particles can comprise a second capture probe that is capable of hybridizing to the capture extenders comprising the second set of capture extenders (and thereby capturing the second target nucleic acid on the second set of particles). In this class of embodiments, detecting the presence of the first and second nucleic acid on the solid support typically includes identifying at least a portion of the particles from each set and detecting the presence of nucleic acid on those particles.

In one aspect, the first target nucleic acid (and optional second, third, etc. target nucleic acid) is captured and its presence on the solid support is detected using a branched-chain DNA (bDNA) assay. Thus, in one class of embodiments, detecting the presence of the first target nucleic acid on the solid support includes hybridizing a first set of one or more label extenders (typically, two or more label extenders) and a label probe system comprising a label to the first target nucleic acid and detecting the presence of the label on the solid support. The label probe system typically includes an amplification multimer and a plurality of label probes, wherein the amplification multimer is capable of hybridizing simultaneously to a label extender and to a plurality of label probes. In another aspect, the label probe system includes a preamplifier, a plurality of amplification multimers, and a plurality of label probes, wherein the preamplifier hybridizes to one or more label extenders, and the amplification multimers hybridize to the preamplifier and to the plurality of label probes. As another example, the label probe system can include only label probes, which hybridize directly to the label extenders. The label probe can include the label, or it can be configured to bind to the label. Suitable labels include, but are not limited to, an enzyme or a fluorescent label. When an enzyme (e.g., alkaline phosphatase) is used as the label, its presence on the solid support can be detected by detecting its activity with a chemiluminescent, colorimetric, or similar assay as is well-known in the art. When a fluorescent label is used, detecting the presence of the label on the solid support typically comprises detecting a fluorescent signal from the label.

At any of various steps in the methods, materials not captured on the solid support are optionally separated from the support (and thus from any support-bound materials). The methods are optionally used to quantitate the amount of the first (and optional second, third, etc.) nucleic acid present in the whole blood sample. Thus, in one class of embodiments, detecting the presence of the first target nucleic acid on the solid support comprises detecting an amount of the first target nucleic acid on the solid support. It will be evident that the amount of the target nucleic acid captured on the solid support is proportional to the amount of the target nucleic acid present in the original sample.

Another general class of embodiments provides methods of detecting at least a first target nucleic acid from plasma. In the methods, plasma comprising the first target nucleic acid is provided. The plasma is contacted with a first set of n capture extenders, wherein n is at least two. The first set of capture extenders is capable of hybridizing to the first target nucleic acid. The first target nucleic acid is hybridized to the first set of capture extenders, and the first set of capture extenders is associated with a solid support. The first target nucleic acid is captured on the solid support by hybridizing the first target nucleic acid to the first set of capture extenders and associating the first set of capture extenders with the solid support. The presence of the first target nucleic acid on the solid support is then detected. The hybridization and association steps can be, e.g., either simultaneous or sequential. In one class of embodiments, the methods include contacting the plasma with an exogenously supplied protease, typically prior to contacting the plasma with the first set of capture extenders.

Essentially all of the features noted for the methods above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, type of solid support, association of the capture extenders with the solid support, detection technique, composition of the optional label probe system, type of label, inclusion of blocking probes, type of target nucleic acid(s), quantitation of the target nucleic acid(s), separation of unbound materials from the solid support, and/or the like.

For example, in one preferred class of embodiments, a first capture probe is bound to the solid support, and associating the first set of capture extenders with the solid support comprises hybridizing the capture extenders to the first capture probe. As another example, the presence of the first target nucleic acid on the solid support is optionally detected by hybridizing a first set of one or more label extenders and a label probe system comprising a label to the first target nucleic acid and then detecting the presence of the label on the solid support.

As for the embodiments above, the methods can be conveniently multiplexed to detect two or more target nucleic acids simultaneously. Thus, in one class of embodiments, the plasma comprises a second target nucleic acid and the methods include contacting the second target nucleic acid with a second set of m capture extenders, wherein m is at least two; this second set of capture extenders is capable of hybridizing to the second target nucleic acid. The second target nucleic acid is hybridized to the second set of capture extenders, and the second set of capture extenders is associated with the solid support. Hybridizing the second target nucleic acid to the second set of capture extenders and associating the second set of capture extenders with the solid support captures the second target nucleic acid on the solid support. The presence of the second target nucleic acid on the solid support is then detected. It will be evident that n, the number of capture extenders in the first set, can but need not be the same as m, the number of capture extenders in the second set. As for the first target nucleic acid, the second target nucleic acid can be essentially any type of nucleic acid. It will be evident that third, fourth, fifth, etc. target nucleic acids are optionally also detected.

In one class of embodiments, the solid support is a substantially planar solid support, the first target nucleic acid is captured at a first selected position on the solid support, and the second target nucleic acid is captured at a second selected position on the solid support. For example, the first set of capture extenders can be hybridized to a first capture probe predisposed at the first selected position, while the second set of capture extenders is hybridized to a second capture probe predisposed at the second selected position.

In another class of embodiments, the solid support comprises a population of particles. The population includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first target nucleic acid is captured on a first set of the particles, and the second target nucleic acid is captured on a second set of the particles. For example, the first set of particles can comprise a first capture probe that is capable of hybridizing to the capture extenders comprising the first set of capture extenders (and thereby capturing the first target nucleic acid on the first set of particles), and the second set of particles can comprise a second capture probe that is capable of hybridizing to the capture extenders comprising the second set of capture extenders (and thereby capturing the second target nucleic acid on the second set of particles). In this class of embodiments, detecting the presence of the first and second nucleic acid on the solid support typically includes identifying at least a portion of the particles from each set and detecting the presence of nucleic acid on those particles.

Compositions related to the methods form another feature of the invention. Thus, one general class of embodiments provides a composition that includes a first set of n capture extenders, wherein n is at least two, and peripheral blood cell nucleic acids. The first set of capture extenders is capable of hybridizing to a first target nucleic acid. The first set of capture extenders is associated with, or is capable of being associated with, a solid support.

In one class of embodiments, the composition includes a whole blood lysate comprising the peripheral blood cell nucleic acids. The composition can include the first target nucleic acid. The peripheral blood cell nucleic acids optionally comprise the first target nucleic acid; alternatively, the first target nucleic acid can, e.g., be a nucleic acid found in the plasma.

In one class of embodiments, the composition includes an exogenously supplied protease. The composition optionally also includes reagents used to detect the first target nucleic acid. For example, in one class of embodiments, the composition includes a label probe system comprising a label and/or a first set of one or more label extenders, which first set of label extenders is capable of hybridizing to the first target nucleic acid.

The composition can include the solid support. The capture extenders are optionally bound to the solid support, e.g., covalently or noncovalently, directly or through a linker. In one preferred class of embodiments, a first capture probe is bound to the solid support. The first capture probe is capable of hybridizing to the capture extenders of the first set of capture extenders and thereby associating the capture extenders with the solid support. As noted above, the solid support can be essentially any suitable support, including any of a variety of materials, configurations, and the like. For example, in one class of embodiments, the solid support is a substantially planar solid support. In another class of embodiments, the solid support comprises a plurality of particles.

The composition optionally includes a second set of m capture extenders, wherein m is at least two. The second set of capture extenders is capable of hybridizing to a second target nucleic acid, and the second set of capture extenders is associated with, or is capable of being associated with, the solid support. In one class of embodiments, the solid support is a substantially planar solid support, wherein the first set of capture extenders is associated with or is capable of being associated with a first selected position on the solid support, and wherein the second set of capture extenders is associated with or is capable of being associated with a second selected position on the solid support. A first capture probe is optionally bound to the solid support at the first selected position while a second capture probe is bound to the solid support at the second selected position. In another class of embodiments, the solid support comprises a population of particles that includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first set of capture extenders is associated with or is capable of being associated with a first set of the particles, and the second set of capture extenders is associated with or is capable of being associated with a second set of the particles. Optionally, the first set of particles comprises a first capture probe capable of hybridizing to the capture extenders comprising the first set of capture extenders, while the second set of particles comprises a second capture probe capable of hybridizing to the capture extenders comprising the second set of capture extenders. The composition optionally includes the second target nucleic acid. It will be evident that the composition optionally also includes third, fourth, fifth, etc. target nucleic acids, sets of capture extenders, sets of particles or selected positions on the solid support, and/or the like.

Essentially all of the features noted for the methods above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, composition of the label probe system, type of label, inclusion of blocking probes, type of target nucleic acid(s), and/or the like.

Another general class of embodiments provides a composition that includes a first set of n capture extenders, wherein n is at least two, and plasma. The first set of capture extenders is capable of hybridizing to a first target nucleic acid. The first set of capture extenders is associated with, or is capable of being associated with, a solid support.

The composition can include the first target nucleic acid (e.g., a DNA or RNA). In one class of embodiments, the composition includes an exogenously supplied protease. The composition optionally also includes reagents used to detect the first target nucleic acid. For example, in one class of embodiments, the composition includes a label probe system comprising a label and/or a first set of one or more label extenders, which first set of label extenders is capable of hybridizing to the first target nucleic acid.

The composition can include the solid support. In one class of embodiments, a first capture probe is bound to the solid support. The first capture probe is capable of hybridizing to the capture extenders of the first set of capture extenders and thereby associating the capture extenders with the solid support. As noted above, the solid support can be essentially any suitable support, including any of a variety of materials, configurations, and the like. For example, in one class of embodiments, the solid support is a substantially planar solid support, while in other embodiments, the solid support comprises a plurality of particles.

The composition optionally includes a second set of m capture extenders, wherein m is at least two. The second set of capture extenders is capable of hybridizing to a second target nucleic acid, and the second set of capture extenders is associated with, or is capable of being associated with, the solid support. In one class of embodiments, the solid support is a substantially planar solid support, wherein the first set of capture extenders is associated with or is capable of being associated with a first selected position on the solid support, and wherein the second set of capture extenders is associated with or is capable of being associated with a second selected position on the solid support. A first capture probe is optionally bound to the solid support at the first selected position while a second capture probe is bound to the solid support at the second selected position. In another class of embodiments, the solid support comprises a population of particles that includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first set of capture extenders is associated with or is capable of being associated with a first set of the particles, and the second set of capture extenders is associated with or is capable of being associated with a second set of the particles. Optionally, the first set of particles comprises a first capture probe capable of hybridizing to the capture extenders comprising the first set of capture extenders, while the second set of particles comprises a second capture probe capable of hybridizing to the capture extenders comprising the second set of capture extenders. The composition optionally includes the second target nucleic acid. It will be evident that the composition optionally also includes third, fourth, fifth, etc. target nucleic acids, sets of capture extenders, sets of particles or selected positions on the solid support, and/or the like.

Essentially all of the features noted for the embodiments above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, composition of the label probe system, type of label, inclusion of blocking probes, type of target nucleic acid(s), and/or the like.

Yet another general class of embodiments provides a kit for detecting at least a first target nucleic acid. The kit includes a first capture probe bound to a solid support, a first set of n capture extenders, wherein n is at least two, a label probe system comprising a label, a first set of one or more label extenders, a first solution comprising a detergent, and a protease, packaged in one or more containers. Instructions for detecting the first target nucleic acid in whole blood, in peripheral blood cells, and/or in plasma with the kit are typically also included. The first set of capture extenders is capable of hybridizing to the first target nucleic acid and to the first capture probe, and the label extenders of the first set are capable of hybridizing to the first target nucleic acid and to the label probe system.

In one aspect, the kits are configured for multiplex detection of target nucleic acids. Thus, in one class of embodiments, the kit also includes a second capture probe bound to the solid support, a second set of m capture extenders, wherein m is at least two, and a second set of one or more label extenders. The second set of capture extenders is capable of hybridizing to a second target nucleic acid and to the second capture probe, and the label extenders of the second set are capable of hybridizing to the second target nucleic acid and to the label probe system.

Essentially all of the features noted for the embodiments above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, type of solid support, association of the capture extenders with the solid support, composition of the label probe system, type of label, type of target nucleic acid(s), and/or the like.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 schematically illustrates a typical standard bDNA assay.

FIG. 2 Panels A-E schematically depict a multiplex bDNA assay, in which the target nucleic acids are captured on distinguishable subsets of microspheres and then detected.

FIG. 3 Panels A-D schematically depict a multiplex bDNA assay, in which the target nucleic acids are captured at selected positions on a solid support and then detected. Panel A shows a top view of the solid support, while Panels B-D show the support in cross-section.

FIG. 4 Panel A depicts a graph illustrating quantitative detection of GAPDH mRNA in whole blood. Fresh, heparinized whole blood from a healthy donor was lysed and assayed for GAPDH expression using a probe set specific for GAPDH mRNA (diamond). No signal from hybridizing with genomic DNA can be detected using probes designed to bind the antisense strand of the target gene (square). Panel B depicts a graph illustrating GAPDH expression in PAXgene® stabilized whole blood. The nucleic acid pellet formed from PAXgene® stabilized blood was solubilized and assayed for GAPDH expression. Panel C depicts a graph illustrating detection of exogenous in vitro dapB transcripts (IVT) in the presence (diamond) and absence (square) of whole blood lysate. Mean±SD (standard deviation) values are graphed.

FIG. 5 Panels A-C schematically depict an overview of a multiplex bDNA assay.

FIG. 6 Panel A depicts a graph illustrating simultaneous detection of multiple genes in the multiplexed assay. A mixture of 9 target IVTs was serially diluted, added to lysate produced from 20 μl whole blood, and assayed using the multiplexed bead assay. MFI: mean fluorescent intensity. Panel B depicts a graph illustrating specificity of multiplex detection. A mixture of 9 target IVTs were assayed simultaneously using the multiplexed bead assay. Signals for E. coli DapB transcript detected in the absence (square) or presence (diamond) of lysate produced from 20 μl human whole blood are shown. LOD for this target is 0.04 attomole. Panel C depicts a bar graph illustrating simultaneous detection of multiple cytokine mRNAs in LPS stimulated whole blood. Whole blood was incubated at 37° C. for 125 min with or without LPS. Sixteen microliters were removed and assayed in multiplex for cytokine gene expressions. Control is blood sample at t₀. Mean+s.d. (standard deviation) values are shown. Panel D depicts a bar graph illustrating simultaneous detection of multiple mRNAs associated with antigen presenting cell activation, detected as described in Panel C. Panel E depicts graphs illustrating consistent measurement of cytokines in LPS activated whole blood using singleplex (left axis, bar graph) and multiplex (right axis, line graph) assay formats. Panel F depicts a graph illustrating GAPDH expression during LPS stimulation of whole blood. Mean+s.d values are shown. Panel G depicts a graph illustrating IL-1 beta expression during LPS stimulation of whole blood.

FIG. 7 Panel A depicts a graph illustrating correlation of the gene expression pattern in whole blood and red blood cell (RBC)-lysed blood. Signals are mean fluorescent intensities. Panel B depicts a graph illustrating correlation of the gene expression pattern between whole blood lysate and RNA. Panel C depicts a graph illustrating correlation of gene expression patterns between whole blood lysate and lysate from PAXgene® blood pellet. Panel D depicts a bar graph illustrating that PAXgene® reagent induces gene expression in whole blood. Error bar: s.d. Data is representative of assays of three independent samples.

Schematic figures are not necessarily to scale.

DEFINITIONS

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. The following definitions supplement those in the art and are directed to the current application and are not to be imputed to any related or unrelated case, e.g., to any commonly owned patent or application. Although any methods and materials similar or equivalent to those described herein can be used in the practice for testing of the present invention, the preferred materials and methods are described herein. Accordingly, the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.

As used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a molecule” includes a plurality of such molecules, and the like.

The term “about” as used herein indicates the value of a given quantity varies by +/−10% of the value, or optionally +/−5% of the value, or in some embodiments, by +/−1% of the value so described.

“Whole blood” is blood from which no constituent (e.g., plasma, platelets, or red blood cells) has been removed. Whole blood optionally includes an exogenously added anticoagulant. Whole blood can be obtained, e.g., from a human or from an animal.

“Peripheral blood cells” are the cellular components of blood, including red blood cells, white blood cells, and platelets. Peripheral blood cells typically include those cells found within the circulating pool of blood and not sequestered within the lymphatic system, spleen, liver, or bone marrow. Within a given sample of peripheral blood cells, all types of blood cells (e.g., red blood cells, white blood cells, and platelets) are represented or potentially represented; no cell type has been deliberately enriched in or removed from the sample.

“Peripheral blood cell nucleic acids” are nucleic acids (e.g., RNA and/or DNA) obtained from a sample of peripheral blood cells. Nucleic acids from all types of blood cells (e.g., red blood cells, white blood cells, and platelets) are represented or potentially represented, no cell type having been deliberately enriched in or removed from the sample of peripheral blood cells from which the nucleic acids were obtained.

“Plasma” is the liquid component of whole blood, in which the peripheral blood cells are suspended. Plasma is typically obtained by centrifuging whole blood to separate the plasma from the blood cells, optionally after addition of an anticoagulant.

A “target nucleic acid” is a nucleic acid to be detected.

The term “polynucleotide” (and the equivalent term “nucleic acid”) encompasses any physical string of monomer units that can be corresponded to a string of nucleotides, including a polymer of nucleotides (e.g., a typical DNA or RNA polymer), peptide nucleic acids (PNAs), modified oligonucleotides (e.g., oligonucleotides comprising nucleotides that are not typical to biological RNA or DNA, such as 2′-O-methylated oligonucleotides), and the like. The nucleotides of the polynucleotide can be deoxyribonucleotides, ribonucleotides or nucleotide analogs, can be natural or non-natural, and can be unsubstituted, unmodified, substituted or modified. The nucleotides can be linked by phosphodiester bonds, or by phosphorothioate linkages, methylphosphonate linkages, boranophosphate linkages, or the like. The polynucleotide can additionally comprise non-nucleotide elements such as labels, quenchers, blocking groups, or the like. The polynucleotide can be, e.g., single-stranded or double-stranded.

A “polynucleotide sequence” or “nucleotide sequence” is a polymer of nucleotides (an oligonucleotide, a DNA, a nucleic acid, etc.) or a character string representing a nucleotide polymer, depending on context. From any specified polynucleotide sequence, either the given nucleic acid or the complementary polynucleotide sequence (e.g., the complementary nucleic acid) can be determined.

Two polynucleotides “hybridize” when they associate to form a stable duplex, e.g., under relevant assay conditions. Nucleic acids hybridize due to a variety of well characterized physico-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking and the like. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, part I chapter 2, “Overview of principles of hybridization and the strategy of nucleic acid probe assays” (Elsevier, New York), as well as in Ausubel, infra.

The term “complementary” refers to a polynucleotide that forms a stable duplex with its “complement,” e.g., under relevant assay conditions. Typically, two polynucleotide sequences that are complementary to each other have mismatches at less than about 20% of the bases, at less than about 10% of the bases, preferably at less than about 5% of the bases, and more preferably have no mismatches.

A first polynucleotide that is “capable of hybridizing” (or “configured to hybridize”) to a second polynucleotide comprises a first polynucleotide sequence that is complementary to a second polynucleotide sequence in the second polynucleotide.

A “capture extender” or “CE” is a polynucleotide that is capable of hybridizing to a nucleic acid of interest, and that is preferably also capable of hybridizing to a capture probe. The capture extender typically has a first polynucleotide sequence C-1, which is complementary to the capture probe, and a second polynucleotide sequence C-3, which is complementary to a polynucleotide sequence of the nucleic acid of interest. Sequences C-1 and C-3 are typically not complementary to each other. The capture extender is preferably single-stranded.

A “capture probe” or “CP” is a polynucleotide that is capable of hybridizing to at least one capture extender and that is tightly bound (e.g., covalently or noncovalently, directly or through a linker, e.g., streptavidin-biotin or the like) to a solid support, a spatially addressable solid support, a slide, a particle, a microsphere, or the like. The capture probe typically comprises at least one polynucleotide sequence C-2 that is complementary to polynucleotide sequence C-1 of at least one capture extender. The capture probe is preferably single-stranded.

A “label extender” or “LE” is a polynucleotide that is capable of hybridizing to a nucleic acid of interest and to a label probe system. The label extender typically has a first polynucleotide sequence L-1, which is complementary to a polynucleotide sequence of the nucleic acid of interest, and a second polynucleotide sequence L-2, which is complementary to a polynucleotide sequence of the label probe system (e.g., L-2 can be complementary to a polynucleotide sequence of an amplification multimer, a preamplifier, a label probe, or the like). The label extender is preferably single-stranded.

A “label” is a moiety that facilitates detection of a molecule. Common labels in the context of the present invention include fluorescent, luminescent, light-scattering, and/or colorimetric labels. Suitable labels include enzymes and fluorescent moieties, as well as radionuclides, substrates, cofactors, inhibitors, chemiluminescent moieties, magnetic particles, and the like. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241. Many labels are commercially available and can be used in the context of the invention.

A “label probe system” comprises one or more polynucleotides that collectively comprise a label and a polynucleotide sequence M-1, which is capable of hybridizing to at least one label extender. The label provides a signal, directly or indirectly. Polynucleotide sequence M-1 is typically complementary to sequence L-2 in the label extenders. Typically, the label probe system includes a plurality of label probes (e.g., a plurality of identical label probes) and an amplification multimer; it optionally also includes a preamplifier or the like, or optionally includes only label probes, for example.

An “amplification multimer” is a polynucleotide comprising a plurality of polynucleotide sequences M-2, typically (but not necessarily) identical polynucleotide sequences M-2. Polynucleotide sequence M-2 is complementary to a polynucleotide sequence in the label probe. The amplification multimer also includes at least one polynucleotide sequence that is capable of hybridizing to a label extender or to a nucleic acid that hybridizes to the label extender, e.g., a preamplifier. For example, the amplification multimer optionally includes at least one polynucleotide sequence M-1; polynucleotide sequence M-1 is typically complementary to polynucleotide sequence L-2 of the label extenders. Similarly, the amplification multimer optionally includes at least one polynucleotide sequence that is complementary to a polynucleotide sequence in a preamplifier. The amplification multimer can be, e.g., a linear or a branched nucleic acid. As noted for all polynucleotides, the amplification multimer can include modified nucleotides and/or nonstandard internucleotide linkages as well as standard deoxyribonucleotides, ribonucleotides, and/or phosphodiester bonds. Suitable amplification multimers are described, for example, in U.S. Pat. No. 5,635,352, U.S. Pat. No. 5,124,246, U.S. Pat. No. 5,710,264, and U.S. Pat. No. 5,849,481.

A “label probe” or “LP” is a single-stranded polynucleotide that comprises a label (or optionally that is configured to bind to a label) that directly or indirectly provides a detectable signal. The label Probe typically comprises a polynucleotide sequence that is complementary to the repeating polynucleotide sequence M-2 of the amplification multi mer; however, if no amplification multimer is used in the bDNA assay, the label probe can, e.g., hybridize directly to a label extender.

A “preamplifier” is a nucleic acid that serves as an intermediate between at least one label extender and amplification multimer. Typically, the preamplifier is capable of hybridizing simultaneously to at least one label extender and to a plurality of amplification multimers.

The “T_(m)” (melting temperature) of a nucleic acid duplex under specified conditions (e.g., relevant assay conditions) is the temperature at which half of the base pairs in a population of the duplex are disassociated and half are associated. The T_(m) for a particular duplex can be calculated and/or measured, e.g., by obtaining a thermal denaturation curve for the duplex (where the T_(m) is the temperature corresponding to the midpoint in the observed transition from double-stranded to single-stranded form).

A “microsphere” is a small spherical, or roughly spherical, particle. A microsphere typically has a diameter less than about 1000 micrometers (e.g., less than about 100 micrometers, optionally less than about 10 micrometers).

A “microorganism” is an organism of microscopic or submicroscopic size. Examples include, but are not limited to, bacteria, fungi, yeast, protozoans, microscopic algae (e.g., unicellular algae), viruses (which are typically included in this category although they are incapable of growth and reproduction outside of host cells), subviral agents, viroids, and mycoplasma.

A variety of additional terms are defined or otherwise characterized herein.

DETAILED DESCRIPTION

Analysis of gene expression in peripheral blood has been increasingly used for diagnosis, prognosis, tracking, and drug response monitoring of hematological diseases (Haferlach, T. et al. (2005) “A global approach to the diagnosis of leukemia using gene expression profiling” Blood 106:1189-1198; Lossos, I. S. et al. (2004) “Prediction of Survival in Diffuse Large-B-Cell Lymphoma Based on the Expression of Six Genes” N Engl J Med 350:1828-1837; Goerttler, P. S. et al. (2005) “Gene expression profiling in polycythaemia vera: overexpression of transcription factor NF-E2” Br J Haematol 129:138-50; Hochhaus, A. et al. (2000) “Detection and quantification of residual disease in chronic myelogenous leukemia” Leukemia 14:998-1005; and Wang, S. W. et al. (1999) “Cytokine mRNA decay is accelerated by an inhibitor of p38-mitogen-activated protein kinase” Inflamm Res 48:533-8). Due to the ease of collection of peripheral blood and its key role in the immune response, peripheral blood gene expression is also being explored for surrogate biomarker discovery in a wide range of non-hematological disorders (DePrimo, S. et al. (2003) “Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification” BMC Cancer 3:3; Gibbs, P. J. et al. (2005) “Quantitative detection of changes in cytokine gene expression in peripheral blood mononuclear cells correlates with and precedes acute rejection in renal transplant recipients” Transpl Immunol 14:99-108; Ockenhouse, C. F. et al. (2005) “Functional Genomic Relationships in HIV-1 Disease Revealed by Gene-Expression Profiling of Primary Human Peripheral Blood Mononuclear Cells” J Infect Dis 191:2064-74; van Leeuwen, D. M. et al. (2005) “Differential Gene Expression in Human Peripheral Blood Mononuclear Cells Induced by Cigarette Smoke and Its Constituents” Toxicol. Sci. 86:200-210; and Horwitz, P. A. et al. (2004) “Detection of Cardiac Allograft Rejection and Response to Immunosuppressive Therapy With Peripheral Blood Gene Expression” Circulation 110:3815-3821). However, validity and reproducibility of blood mRNA quantitation results are critical issues when considering potential clinical applications (Ransohoff, D. F. (2005) “Bias as a threat to the validity of cancer molecular-marker research” Nat Rev Cancer 5:142-9, and Ransohoff, D. F. (2004) “Rules of evidence for cancer molecular-marker discovery and validation” Nat Rev Cancer 4:309-14), and indeed, limitations associated with the techniques currently used in peripheral blood gene expression analysis have hindered wider application of genomics advances in the clinic (Pahl, A. (2005) “Gene expression profiling using RNA extracted from whole blood: technologies and clinical applications” Expert Rev Mol Diagn 5:43-52, and Bustin, S. A. et al. (2005) “Quantitative real-time RT-PCR—a perspective” J Mol Endocrinol 34:597-601). Robust, reproducible gene expression analysis in peripheral blood has been a challenge (Fan, H. and Hegde, P. S. (2005) “The transcriptome in blood: challenges and solutions for robust expression profiling” Curr Mol Med 5:3-10).

One major source of variation that is unique to peripheral blood mRNA analysis is the pre-analytical handling of the blood sample. Using current techniques for expression analysis, gene expression patterns are strongly dependent on choice of blood isolation and RNA preparation techniques (Fan and Hegde, supra, and Debey, S. et al. (2004) “Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types” Pharmacogenomics J 4:193-207). Partial purification of blood cells via density gradient centrifugation or selective red cell lysis can change gene expression, as blood cells are known to be sensitive to external environmental stress (Hartel, C. et al. (2001) “Ex vivo induction of cytokine mRNA expression in human blood samples” J Immunol Methods 249:63-71; Tamul, K. R. et al. (1995) “Comparison of the effects of Ficoll-Hypaque separation and whole blood lysis on results of immunophenotypic analysis of blood and bone marrow samples from patients with hematologic malignancies” Clin Diagn Lab Immunol 2:337-42; Whitney, A. R. et al. (2003) “Individuality and variation in gene expression patterns in human blood” Proc Natl Acad Sci USA 100:1896-901; Rainen, L. et al. (2002) “Stabilization of mRNA Expression in Whole Blood Samples” Clin Chem 48:1883-1890; and Stordeur, P., Zhou, L. and Goldman, M. (2002) “Analysis of spontaneous mRNA cytokine production in peripheral blood” J Immunol Methods 261:195-7). Furthermore, significant gene expression changes can be detected within hours after phlebotomy, even without additional handling (Rainen et al., supra, and Tanner, M. A. et al. (2002) “Substantial changes in gene expression level due to the storage temperature and storage duration of human whole blood” Clinical and Laboratory Haematology 24:337-341). One way to minimize variations caused by storage and manipulation is to extract total RNA from fresh whole blood using phenol-chloroform extraction. However, this approach suffers from interference from the high concentration of plasma and erythrocyte proteins, leading to inconsistent yield and quality of the resulting purified RNA (Feezor, R. J. et al. (2004) “Whole blood and leukocyte RNA isolation for gene expression analyses” Physiol. Genomics 19:247-254). In addition, contaminating genomic DNA or PCR inhibitors such as heparin in the resulting purified RNA can reduce the accuracy of subsequent real-time quantitative PCR (RT-PCR) analysis (e.g., Bustin, S. A. and Nolan, T. (2004) “Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction” J Biomol Tech 15:155-66), and the highly abundant red cell specific RNA can affect microarray profiling (Debey et al., supra).

Use of the blood-stabilizing reagent PAXgene® prior to RNA purification from the blood can prevent RNA degradation and time-dependent ex vivo induction of cytokine and immediate early response genes (Rainen et al., supra). However, signal to noise ratios are significantly reduced in microarray expression profiles of PAXgene®-treated blood RNA (Wu, K. et al. (2003) “Globin reduction protocol” Affymetrix Technical Note, available at www (dot) affymetrix (dot) com/support/technotes/blood2_technote (dot) pdf). In addition, the overall gene expression pattern from PAXgene® stabilized whole blood is quite distinct from that of the leukocytes (Feezor et al., supra). This difference has been attributed to the presence of an overwhelming amount of globin mRNA originating from the reticulocytes and remaining in the RNA purified from PAXgene®-treated blood; however, selective removal of globin mRNAs from PAXgene® purified RNA could not recover the leukocyte expression pattern (Feezor et al., supra). PAXgene®-treated blood appears to give a low and variable yield of purified RNA, and the storage time of the PAXgene®-treated blood appears to significantly affect subsequent microarray profiling results as well, suggesting that stabilization is a complex process (Muller, M. C. et al. (2004) “Standardization of preanalytical factors for minimal residual disease analysis in chronic myelogenous leukemia” Acta Haematol 112:30-3; Thach, D. C. et al. (2003) “Assessment of two methods for handling blood in collection tubes with RNA stabilizing agent for surveillance of gene expression profiles with high density microarrays” J Immunol Methods 283:269-79; and Wang, J. et al. (2004) “Optimizing RNA extraction yield from whole blood for microarray gene expression analysis” Clin Biochem 37:741-4). In addition, the effect of PAXgene® treatment of blood samples on the expression of genes other than the dozen genes examined in Rainen et al., supra, has not been reported.

Currently, microarray analysis and RT-PCR are the most widely used methods for analyzing gene expression in blood. The relatively long experimental procedure and moderate sensitivity of microarrays have limited their use in high throughput expression profiling applications. More importantly, despite the high technical reproducibility of commercial microarrays, the overall reproducibility of the microarray data between runs, between laboratories, and between platforms is generally poor (Chen, J. J. et al. (2004) “Analysis of variance components in gene expression data” Bioinformatics 20:1436-1446; Kuo, W. P. et al. (2002) “Analysis of matched mRNA measurements from two different microarray technologies” Bioinformatics 18:405-12; Marshall, E. (2004) “Getting the noise out of gene arrays” Science 306:630-631; and Bammler, T. et al. (2005) “Standardizing global gene expression analysis between laboratories and across platforms” Nat Methods 2:351-6). Different blood RNA isolation procedures and different RNA labeling and amplification protocols used in different laboratories can give strikingly different expression patterns for even identical starting material (Feezor et al., supra, and Bammler, T. et al. (2005) “Standardizing global gene expression analysis between laboratories and across platforms” Nat Methods 2:351-6). Thus, significant variations can result, not necessarily from microarray hybridization itself, but from the processing steps used to prepare labeled RNA for hybridization.

RT-PCR offers greater sensitivity than microarray analysis, and it is widely used to validate microarray results. It has been used for quantitating specific mRNA levels in blood (Stordeur, P., Zhou, L. and Goldman, M. (2002) “Analysis of spontaneous mRNA cytokine production in peripheral blood” J Immunol Methods 261:195-7), but the approach has low multiplex capabilities. Moreover, as with microarray analysis, RT-PCR depends on purification and enzymatic manipulation (e.g., reverse transcription and subsequent amplification) of RNA from the blood. Variation in the overall quality of the RNA and in the efficiencies of reverse transcription and PCR are major factors that can reduce the accuracy and reproducibility of mRNA quantitation by RT-PCR (Bustin, S. A. and Nolan, T. (2004) “Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction” J Biomol Tech 15:155-66 and Bustin, S. A. et al. (2002) “Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems” J Mol Endocrinol 29:23-39). In practice, RT-PCR quantitation of BCR-ABL mRNA in patients with chronic myelogenous leukemia has been affected by variations in sample preparation (Muller, M. C. et al. (2004) “Standardization of preanalytical factors for minimal residual disease analysis in chronic myelogenous leukemia” Acta Haematol 112:30-3).

Even typical techniques for mRNA detection that do not require prior purification of RNA (see, e.g., Martel et al. (2002) “Multiplexed screening assay for mRNA combining nuclease protection with luminescent array detection” Assay and Drug Development Technologies 1:61-71; E is et al. (2001) “An invasive cleavage assay for direct quantitation of specific RNAs”. Nature Biotechnology 19:673-676; and Tian et al. (2004) “Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis” Nucl Acids Res 32:e126) involve enzymatic manipulation of the RNA, and are thus subject to variability, have limited sensitivity, and/or require specialized probes, equipment, and data analysis software. In addition, such techniques may not all be suitable for use with whole blood samples.

In contrast, the present invention provides methods that permit rapid, simple, and sensitive detection of mRNAs (and other nucleic acids) from whole blood, without requiring isolation of a particular blood cell type, purification of RNA, and/or enzymatic manipulation of RNA. Following lysis of the blood cells, typically, in a sample of whole blood, one or more target nucleic acids are captured on a solid support and then detected, for example, using a branched-chain DNA (bDNA) assay. Methods for detecting nucleic acids directly from blood plasma are also provided, as are compositions and kits related to the methods. The methods of the invention are optionally used for gene expression analysis, clinical diagnosis, and/or detection of microorganisms, e.g., pathogens, among other applications.

Methods for Detecting Nucleic Acids from Blood

One general class of embodiments provides methods of detecting at least a first target nucleic acid. In the methods, a sample comprising whole blood is provided. The whole blood includes peripheral blood cells, which are lysed to produce a lysate comprising the first target nucleic acid. The first target nucleic acid is contacted with a first set of n capture extenders, wherein n is at least two; this first set of capture extenders is capable of hybridizing to the first target nucleic acid. The first target nucleic acid is hybridized to the first set of capture extenders, and the first set of capture extenders is associated with a solid support. The first target nucleic acid is captured on the solid support by hybridizing the first target nucleic acid to the first set of capture extenders and associating the first set of capture extenders with the solid support, and the presence of the first target nucleic acid on the solid support is then detected. The hybridization and association steps can, e.g., be either simultaneous or sequential.

Typically, the first target nucleic acid is contacted with the first set of capture extenders by contacting the lysate with the first set of capture extenders. The peripheral blood cells are optionally separated from the plasma (e.g., by centrifugation) prior to lysis of the peripheral blood cells, to provide a peripheral blood cell lysate; contacting the first target nucleic acid with the first set of capture extenders then comprises contacting the peripheral blood cell lysate with the first set of capture extenders. However, such separation is not necessary. Thus, in one class of embodiments, the peripheral blood cells are lysed in the whole blood (e.g., liquid whole blood) to produce a whole blood lysate that includes the first target nucleic acid (e.g., among other nucleic acids released from the peripheral blood cells and/or present in the plasma). In this class of embodiments, contacting the first target nucleic acid with the first set of capture extenders typically comprises contacting the whole blood lysate with the first set of capture extenders. Alternatively but less conveniently, nucleic acids (e.g., total nucleic acids, total RNA, total DNA, or the like) including the first target nucleic acid can be purified or partially purified from the lysate prior to contact with the capture extenders. For example, nucleic acids can be isolated from the whole blood lysate (or the peripheral blood cell lysate) by precipitation using techniques known in the art; such precipitated nucleic acids can be resuspended in an appropriate solution (e.g., a buffered aqueous solution) and then contacted with the first set of capture extenders. The whole blood is optionally treated with a stabilizing reagent such as PAXgene® prior to lysis of the peripheral blood cells, but it need not be (and preferably is not).

In one aspect, as described above, the peripheral blood cells are lysed in liquid whole blood to produce the lysate. In another aspect, the target nucleic acid(s) are detected from a dried blood spot. Thus, in one class of embodiments, the whole blood is applied to a matrix to produce a blood spot, and the blood spot is dried (e.g., air dried) to produce a dried blood spot. The dried blood spot is contacted with an aqueous solution to produce the lysate. The solution can comprise a buffered salt solution, a detergent, a protease, and/or the like, as described herein. The matrix to which the blood is applied is typically an absorbent matrix, for example, a specimen collection paper, filter paper, or the like.

A variety of techniques for lysing cells are known in the art and can be adapted to the practice of the present invention. For example, the peripheral blood cells can be lysed by contact with a detergent (e.g., an anionic detergent such as lithium lauryl sulfate), suspension in a low ionic strength buffer, sonication, freeze-thaw cycles, or a combination thereof.

In one class of embodiments, the methods include contacting the peripheral blood cells and/or the lysate with an exogenously supplied protease (a protease that is added to the peripheral blood cells and/or the lysate by a user of the methods, as opposed to a protease which is endogenous to whole blood and is thus already present), typically prior to contacting the first target nucleic acid with the first set of capture extenders. By digesting various blood proteins, the protease optionally inactivates ribonucleases and/or otherwise assists in increasing the integrity and/or availability of the target nucleic acid. A variety of proteases are known in the art and can be adapted to the practice of the present invention; an effective concentration of protease, time for which the lysate is incubated with the protease, and the like can be determined by routine experimentation, e.g., by ensuring that an exogenously added RNA can be quantitatively detected in the lysate.

In one embodiment, the protease is proteinase K. Proteinase K is commercially available from a number of suppliers, and it has little dependence on cofactors, remains active in the presence of fairly high concentrations of detergent (e.g., lithium lauryl sulfate or the like used to lyse the peripheral blood cells), and is active at elevated temperatures. In the example described below, proteinase K is employed at a concentration of at least 1 mg per ml of lysate; it will be evident that the concentration of protease can readily be varied, e.g., in conjunction with the duration of time for which the cells and/or lysate is incubated with the protease.

The volume of blood used in the assay is typically less than the volume of the resulting lysate, optionally substantially less. Thus, in one class of embodiments, the volume of whole blood in the sample is at most ½, at most ⅓, or at most ⅕ the volume of the lysate. For example, the volume of whole blood used can be at most 1/10, 1/50, 1/100, or 1/150 the volume of the lysate. The remainder of the volume of the lysate can comprise a buffered salt solution, a detergent, a protease, water, and/or the like.

The methods can be applied to detection of essentially any type of nucleic acids. For example, the first target nucleic acid can be a DNA or an RNA, e.g., an mRNA, rRNA, microRNA precursor, or essentially any other form of RNA. A target nucleic acid can, for example, be expressed by a peripheral blood cell or by an intracellular or extracellular pathogen, and can be located in the peripheral blood cells and/or in the plasma. Thus, in one class of embodiments, the peripheral blood cells include white blood cells, one or more of which white blood cells comprises the first target nucleic acid. The first target nucleic acid can, e.g., be endogenous to the white blood cells or it can be expressed as a result of infection of the white blood cells by a virus, bacterium, or other pathogen. The first target nucleic acid need not be expressed in all types of white blood cells, or even in all cells of a particular type or subtype; for example, the target nucleic acid can be found in one or more of: a granulocyte, mononuclear cell, neutrophil, basophil, eosinophil, monocyte, lymphocyte, T lymphocyte, B lymphocyte, natural killer cell, active granular natural killer cell, inactive agranular natural killer cell, Th-lymphocyte, Tc/k-lymphocyte, activated T cell, activated neutrophil, activated eosinophil, activated basophil, or the like. Similarly, the first target nucleic acid can be found in a red blood cell, platelet, bacterium, virion, or other pathogen.

It will be understood that if the first target nucleic acid is initially present in the whole blood in a double-stranded form, e.g., hybridized to a complementary nucleic acid, the double-stranded form is denatured prior to hybridizing the first target nucleic acid to the first set of capture extenders. Denaturation can be accomplished, for example, by thermal denaturation, exposure to alkaline conditions (which can have the added advantage of digesting extraneous RNA if the target nucleic acid is a DNA), or similar techniques. The methods can thus be used for detecting, e.g., double-stranded genomic DNA, double-stranded viral nucleic acids, and the like, as well as single-stranded nucleic acids such as mRNAs.

As noted, the first set of capture extenders includes n capture extenders, where n is at least two. Preferably, n is at least three, and n can be at least four or at least five or more. Typically, but not necessarily, n is at most ten. For example, n can be between three and ten, e.g., between five and ten or between five and seven, inclusive. Use of fewer capture extenders can be advantageous, for example, in embodiments in which target nucleic acids are to be specifically detected from samples including other nucleic acids with sequences very similar to that of the target nucleic acids. In other embodiments (e.g., embodiments in which capture of as much of the target nucleic acid as possible is desired), however, n can be more than 10, e.g., between 20 and 50. The n capture extenders in the first set preferably hybridize to nonoverlapping polynucleotide sequences in the first target nucleic acid. The nonoverlapping polynucleotide sequences can, but need not be, consecutive within the first target nucleic acid.

The capture extenders are optionally bound to the solid support, e.g., covalently or noncovalently, directly or through a linker, e.g., streptavidin-biotin or the like. In a preferred aspect, the capture extenders are associated with the solid support by hybridization of the capture extenders to one or more capture probes. Thus, in one class of embodiments, a first capture probe is bound to the solid support, and the first set of capture extenders is associated with the solid support by hybridizing the capture extenders to the first capture probe.

Each capture extender in the first set is capable of hybridizing to the first capture probe. The capture extender typically includes a polynucleotide sequence C-1 that is complementary to a polynucleotide sequence C-2 in the capture probe. C-1 and C-2 are typically, but need not be, 20 nucleotides or less in length. Hybridization of the capture extenders to the capture probe is optionally cooperative, e.g., as described in U.S. patent applications 60/680,976 filed May 12, 2005 and Ser. No. 11/433,081 filed May 11, 2006, both by Luo et al. entitled “Multiplex branched-chain DNA assays.” Thus, hybridizing the first set of capture extenders to the first capture probe is optionally performed at a hybridization temperature which is greater than a melting temperature (T_(m)) of a complex between each individual capture extender and the capture probe. Binding of a single capture extender and any associated nucleic acid to the capture probe is thus typically insufficient to capture the nucleic acid on the solid support.

The capture probe can include polynucleotide sequence in addition to C-2, or C-2 can comprise the entire polynucleotide sequence of the capture probe. For example, each capture probe optionally includes a linker sequence between the site of attachment of the capture probe to the solid support and sequence C-2 (e.g., a linker sequence containing 8 Ts, as just one possible example). Typically, each capture probe includes a single sequence C-2, and each capture extender in the first set includes the same nucleotide sequence as its sequence C-1. A number of other configurations are contemplated, however; for example, the capture probe can include two or more sequences C-2 (of the same or different nucleotide sequence), different capture extenders can include different nucleotide sequences as their sequence C-1, complementary to different sequences C-2 in a single or in different first capture probes, and the like.

The solid support can be essentially any suitable support, including any of a variety of materials, configurations, and the like. For example, in one class of embodiments, the solid support is a substantially planar solid support, e.g., an upper surface of the bottom of a well of a multiwell plate, a slide, or the like. Similarly, suitable solid supports include any surface of a well of a multiwell plate, whether planar or not. As another example, the solid support can comprise a plurality of particles, e.g., microspheres, beads, cylindrical particles, irregularly shaped particles, or the like. The particles are optionally identifiable, as will be described in greater detail below, and optionally have additional or other desirable characteristics. For example, the particles can be magnetic or paramagnetic, providing a convenient means for separating the particles from solution, e.g., to simplify separation of the particles from any materials not bound to the particles.

The methods can be conveniently multiplexed to detect two or more target nucleic acids simultaneously. Thus, in one class of embodiments, the lysate comprises a second target nucleic acid and the methods include contacting the second target nucleic acid with a second set of m capture extenders (e.g., by contacting the lysate with the second set of capture extenders, typically with the first and second sets simultaneously), wherein m is at least two; this second set of capture extenders is capable of hybridizing to the second target nucleic acid. The second target nucleic acid is hybridized to the second set of capture extenders, and the second set of capture extenders is associated with the solid support. Hybridizing the second target nucleic acid to the second set of capture extenders and associating the second set of capture extenders with the solid support captures the second target nucleic acid on the solid support. The presence of the second target nucleic acid on the solid support is then detected. It will be evident that n, the number of capture extenders in the first set, can but need not be the same as m, the number of capture extenders in the second set. As for the first target nucleic acid, the second target nucleic acid can be essentially any type of nucleic acid.

In one class of embodiments, the solid support is a substantially planar solid support, the first target nucleic acid is captured at a first selected position on the solid support, and the second target nucleic acid is captured at a second selected position on the solid support. For example, the first set of capture extenders can be hybridized to a first capture probe predisposed at the first selected position, while the second set of capture extenders is hybridized to a second capture probe predisposed at the second selected position. Techniques for forming such arrays of capture probes are well known and are, e.g., referenced below in the section entitled “Arrays.” Spatially addressable non-planar solid supports can optionally also be employed in the methods. In this class of embodiments, detecting the presence of the first and second nucleic acid on the solid support typically includes detecting the presence of nucleic acid at each selected position on the solid support.

In another class of embodiments, the solid support comprises a population of particles. The population includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first target nucleic acid is captured on a first set of the particles, and the second target nucleic acid is captured on a second set of the particles. For example, the first set of particles can comprise a first capture probe that is capable of hybridizing to the capture extenders comprising the first set of capture extenders (and thereby capturing the first target nucleic acid on the first set of particles), and the second set of particles can comprise a second capture probe that is capable of hybridizing to the capture extenders comprising the second set of capture extenders (and thereby capturing the second target nucleic acid on the second set of particles). In this class of embodiments, detecting the presence of the first and second nucleic acid on the solid support typically includes identifying at least a portion of the particles from each set and detecting the presence of nucleic acid on particles from each set.

Essentially any suitable particles, e.g., particles having distinguishable characteristics and to which capture probes can be attached, can be used. For example, in one preferred class of embodiments, the particles are microspheres. The microspheres of each set can be distinguishable from those of the other sets, e.g., on the basis of their fluorescent emission spectrum, their diameter, or a combination thereof. For example, the microspheres of each set can be labeled with a unique fluorescent dye or mixture of such dyes, quantum dots with distinguishable emission spectra, and/or the like. As another example, the particles of each set can be identified by an optical barcode, unique to that set, present on the particles.

It will be evident that third, fourth, fifth, etc. target nucleic acids are optionally also detected. The at least one target nucleic acid to be detected thus optionally includes two or more, five or more, 10 or more, 20 or more, 30 or more, 40 or more, 50 or more, or even 100 or more target nucleic acids which are present or suspected to be present in the whole blood. A like number of sets of capture extenders, and typically a like number of selected positions on a substantially planar solid support or a like number of sets of particles, are also provided and used to capture and detect the target nucleic acids. For additional details on multiplex bDNA assays, see U.S. patent application No. 60/680,976 filed May 12, 2005 and Ser. No. 11/433,081 filed May 11, 2006, both by Luo et al. entitled “Multiplex branched-chain DNA assays” and the examples below.

The presence of the first target nucleic acid (and optional second, third, etc. nucleic acids) on the solid support can be detected by any of a variety of techniques known in the art. For example, the first target nucleic acid can comprise a label (including, e.g., one or two or more labels per molecule), and detecting the presence of the first target nucleic acid can comprise detecting the label. The label can be covalently associated with the nucleic acid (e.g., a fluorescent label can be incorporated into the nucleic acid using a chemical or enzymatic labeling technique), or the nucleic acid can be configured to bind the label (e.g., a biotinylated nucleic acid can bind a streptavidin-associated label). The label can be essentially any convenient label that directly or indirectly provides a detectable signal. For example, the label can be a fluorescent label (e.g., a quantum dot or fluorophore, e.g., Cy™3 or Cy™5), a luminescent label, a light-scattering label (e.g., colloidal gold particles), or an enzyme (e.g., horseradish peroxidase (HRP) or alkaline phosphatase). As another example, at least one detection probe (a polynucleotide comprising a label or configured to bind a label) can be provided and hybridized to the first target nucleic acid, and detecting the presence of the first target nucleic acid can comprise detecting the label. For example, a labeled molecular dendrimer can be hybridized to the first target nucleic acid, for example, a dendrimer such as 3DNA™ from Genisphere Inc.; an exemplary 3DNA dendrimer includes 1-15 oligonucleotides complementary to the target nucleic acid and 30-900 fluorescent labels such as Cy™3, Cy™5, Alexa Fluor 546 or Alexa Fluor 647. As yet another example, the target nucleic acid can be amplified. A wide variety of techniques for amplifying nucleic acids are known in the art, including, but not limited to, PCR (polymerase chain reaction), rolling circle amplification, and transcription mediated amplification. (See, e.g., Hatch et al. (1999) “Rolling circle amplification of DNA immobilized on solid surfaces and its application to multiplex mutation detection” Genet Anal. 15:35-40; Baner et al. (1998) “Signal amplification of padlock probes by rolling circle replication” Nucleic Acids Res. 26:5073-8; and Nallur et al. (2001) “Signal amplification by rolling circle amplification on DNA microarrays” Nucleic Acids Res. 29:E118.) A labeled primer and/or labeled nucleotides are optionally incorporated during amplification.

In one aspect, the first target nucleic acid (and optional second, third, etc. target nucleic acid) is captured and its presence on the solid support is detected using a branched-chain DNA (bDNA) assay. Thus, in one preferred class of embodiments, detecting the presence of the first target nucleic acid on the solid support includes hybridizing a first set of one or more label extenders (typically, two or more label extenders) and a label probe system comprising a label to the first target nucleic acid and detecting the presence of the label on the solid support. The label probe system optionally includes an amplification multimer and a plurality of label probes, where the amplification multimer is capable of hybridizing simultaneously to a label extender and to a plurality of label probes. In another aspect, the label probe system includes a preamplifier, a plurality of amplification multimers, and a plurality of label probes, wherein the preamplifier hybridizes to a label extender, and the amplification multimers hybridize to the preamplifier and to the plurality of label probes. As another example, the label probe system can include only label probes, which hybridize directly to the label extenders. The label probe can include the label, or it can be configured to bind to the label (for example, a biotinylated label probe can bind to a streptavidin-associated label). Suitable labels include, but are not limited to, an enzyme or a fluorescent label. When an enzyme (e.g., alkaline phosphatase) is used as the label, its activity can be detected with a chemiluminescent, colorimetric, or similar assay as is well-known in the art. When a fluorescent label is used, detecting the presence of the label on the solid support typically comprises detecting a fluorescent signal from the label. Two or more label extenders optionally hybridize to a component of the label probe system (e.g., a single amplification multimer or preamplifier), and such hybridization is optionally cooperative; see U.S. patent application Ser. No. 11/471,025 filed Jun. 19, 2006 by Luo et al. entitled “Multiplex detection of nucleic acids.”

An exemplary embodiment in which a single target nucleic acid is captured and detected using a bDNA assay is schematically illustrated in FIG. 1. Peripheral blood cells in a sample of whole blood are lysed to produce a lysate including first target nucleic acid 114. First target nucleic acid 114 (e.g., an mRNA whose expression is to be detected in whole blood) is captured by capture probe 104 on solid support 101 (e.g., a well of a microtiter plate) through first set 111 of synthetic oligonucleotide capture extenders. Each capture extender has first polynucleotide sequence C-3 (152) that can hybridize to the target nucleic acid and second polynucleotide sequence C-1 (151) that can hybridize to the capture probe through sequence C-2 (150) in the capture probe. Typically, two or more capture extenders are used. Each label extender in first set 121 of label extenders hybridizes to a different sequence on the target nucleic acid, through sequence L-1 (154) that is complementary to the target nucleic acid, and to sequence M-1 (157) on amplification multimer 141, through sequence L-2 (155). Blocking probes, which hybridize to sequences in the target nucleic acid not bound by either capture extenders or label extenders, are often used in bDNA assays to reduce non-specific target probe binding. A probe set for a given target nucleic acid thus consists of capture extenders, label extenders, and optional blocking probes for the target nucleic acid. The capture extenders, label extenders, and optional blocking probes are complementary to nonoverlapping sequences in the target nucleic acid, and are typically, but not necessarily, contiguous. In this example, a single blocking probe is used (124).

Signal amplification begins with the binding of the label extenders to the target nucleic acid. The amplification multimer is then hybridized to the label extenders. The amplification multimer has multiple copies of sequence M-2 (158) that is complementary to label probe 142. (It is worth noting that the amplification multimer is typically, but not necessarily, a branched-chain nucleic acid; for example, the amplification multimer can be a branched, forked, or comb-like nucleic acid or a linear nucleic acid.) Label 143, for example, alkaline phosphatase, is covalently attached to each label probe. (Alternatively, the label can, e.g., be noncovalently associated with the label probes.) In the final step, labeled complexes are detected, e.g., by the alkaline phosphatase-mediated degradation of a chemilumigenic substrate, e.g., dioxetane. Luminescence is reported as relative luminescence units (RLUs) on a microplate reader. The amount of chemiluminescence is proportional to the level of first target nucleic acid originally present in the sample of whole blood.

In the preceding example, the amplification multimer and the label probes comprise label probe system 140. In another example, the label probe system also comprises a preamplifier, e.g., as described in U.S. Pat. No. 5,635,352 and U.S. Pat. No. 5,681,697, which further amplifies the signal from a single target mRNA: See also U.S. patent application Ser. No. 11/471,025. In yet another example, the label extenders hybridize directly to the label probes and no amplification multimer or preamplifier is used, so the signal from a single target mRNA molecule is only amplified by the number of distinct label extenders that hybridize to that mRNA (and the number of label probes that bind to a single label extender).

Basic bDNA assays have been well described and have been used, e.g., to detect and quantify mRNA transcripts in cell lines and to determine viral loads. The bDNA assay provides direct quantification of nucleic acid molecules at physiological levels. Several advantages of the technology distinguish it from other DNA/RNA amplification technologies, including linear amplification, good sensitivity and dynamic range, great precision and accuracy, simple sample preparation procedure, and reduced sample-to-sample variation. For additional details on bDNA assays, see, e.g., U.S. Pat. No. 4,868,105 to Urdea et al. entitled “Solution phase nucleic acid sandwich assay”; U.S. Pat. No. 5,635,352 to Urdea et al. entitled “Solution phase nucleic acid sandwich assays having reduced background noise”; U.S. Pat. No. 5,681,697 to Urdea et al. entitled “Solution phase nucleic acid sandwich assays having reduced background noise and kits therefor”; U.S. Pat. No. 5,124,246 to Urdea et al. entitled “Nucleic acid multimers and amplified nucleic acid hybridization assays using same”; U.S. Pat. No. 5,624,802 to Urdea et al. entitled “Nucleic acid multimers and amplified nucleic acid hybridization assays using same”; U.S. Pat. No. 5,849,481 to Urdea et al. entitled “Nucleic acid hybridization assays employing large comb-type branched polynucleotides”; U.S. Pat. No. 5,710,264 to Urdea et al. entitled “Large comb type branched polynucleotides”; U.S. Pat. No. 5,594,118 to Urdea and Horn entitled “Modified N-4 nucleotides for use in amplified nucleic acid hybridization assays”; U.S. Pat. No. 5,093,232 to Urdea and Horn entitled “Nucleic acid probes”; U.S. Pat. No. 4,910,300 to Urdea and Horn entitled “Method for making nucleic acid probes”; U.S. Pat. No. 5,359,100; U.S. Pat. No. 5,571,670; U.S. Pat. No. 5,614,362; U.S. Pat. No. 6,235,465; U.S. Pat. No. 5,712,383; U.S. Pat. No. 5,747,244; U.S. Pat. No. 6,232,462; U.S. Pat. No. 5,681,702; U.S. Pat. No. 5,780,610; U.S. Pat. No. 5,780,227 to Sheridan et al. entitled “Oligonucleotide probe conjugated to a purified hydrophilic alkaline phosphatase and uses thereof”; U.S. patent application Publication No. US2002172950 by Kenny et al. entitled “Highly sensitive gene detection and localization using in situ branched-DNA hybridization”; Wang et al. (1997) “Regulation of insulin preRNA splicing by glucose” Proc Nat Acad Sci USA 94:4360-4365; Collins et al. (1998) “Branched DNA (bDNA) technology for direct quantification of nucleic acids: Design and performance” in Gene Quantification, F Ferre, ed.; and Wilber and Urdea (1998) “Quantification of HCV RNA in clinical specimens by branched DNA (bDNA) technology” Methods in Molecular Medicine: Hepatitis C 19:71-78. In addition, reagents for performing basic bDNA assays (e.g., QuantiGene® kits, amplification multimers, alkaline phosphatase labeled label probes, chemilumigenic substrate, capture probes immobilized on a solid support, and the like) are commercially available, e.g., from Panomics, Inc. (www (dot) panomics (dot) com), and can be adapted for the practice of the present invention. Software for designing probe sets for a given mRNA target (i.e., for designing the regions of the capture extenders, label extenders, and optional blocking probes that are complementary to the target) is also commercially available (e.g., ProbeDesigner™ from Panomics, Inc.); see also Bushnell et al. (1999) “ProbeDesigner: for the design of probe sets for branched DNA (bDNA) signal amplification assays Bioinformatics 15:348-55.

Another exemplary embodiment is schematically illustrated in FIG. 2. This example demonstrates multiplex capture and detection of target nucleic acids with a bDNA assay, where the solid support comprises a population of particles (in this example, a population of microspheres, where each set of microspheres has a characteristic fluorescent emission spectrum). Panel A illustrates three distinguishable sets of microspheres 201, 202, and 203, which have associated therewith capture probes 204, 205, and 206, respectively. Each capture probe includes a sequence C-2 (250), which is different from set to set of microspheres. The three sets of microspheres are combined to form population 208 (Panel B). A set of three capture extenders is provided for each target nucleic acid; set 211 for nucleic acid 214, set 212 for nucleic acid 215 which is not present, and set 213 for nucleic acid 216. Each capture extender includes sequences C-1 (251, complementary to the respective capture probe's sequence C-2) and C-3 (252, complementary to a sequence in the corresponding target nucleic acid). Three sets of label extenders (221, 222, and 223 for nucleic acids 214, 215, and 216, respectively) and three sets of blocking probes (224, 225, and 226 for nucleic acids 214, 215, and 216, respectively) are also provided. Each label extender includes sequences L-1 (254, complementary to a sequence in the corresponding target nucleic acid) and L-2 (255, complementary to M-1).

The sample comprising whole blood is provided and the peripheral blood cells are lysed, providing a lysate (e.g., a whole blood lysate) including target nucleic acids 214 and 216. Non-target nucleic acids 230 are also present. Target nucleic acids 214 and 216 are contacted with and hybridized to their corresponding set of capture extenders (211 and 213, respectively), and the capture extenders are hybridized to the corresponding capture probes (204 and 206, respectively), capturing target nucleic acids 214 and 216 on microspheres 201 and 203, respectively (Panel C). Materials not bound to the microspheres (e.g., capture extenders 212, nucleic acids 230, etc.) are optionally separated from the microspheres by washing. Label probe system 240 including amplification multimer 241 (which includes sequences M-1 257 and M-2 258) and label probe 242 (which contains label 243) is hybridized to label extenders 221 and 223, which are hybridized to nucleic acids 214 and 216, respectively (Panel D). Materials not captured on the microspheres are optionally removed by washing the microspheres. Microspheres from each set are identified, e.g., by their fluorescent emission spectrum (λ₂ and λ₃, Panel E), and the presence or absence of the label on each set of microspheres is detected (λ₁, Panel E). (It is worth noting that in embodiments such as this, in which both the label and the particles are fluorescent, fluorescent emission by the label is typically distinguishable from fluorescent emission by the particles, e.g., microspheres, and many suitable fluorescent label-fluorescent microsphere combinations are possible.) Since each target nucleic acid is associated with a distinct set of microspheres via hybridization with the corresponding set of capture extenders and capture probe, the presence of the label on a given set of microspheres correlates with the presence of the corresponding target nucleic acid on the microspheres and thus in the original sample.

As depicted in FIG. 2, all of the label extenders in all of the sets typically include an identical sequence L-2. Optionally, however, different label extenders (e.g., label extenders in different sets) can include different sequences L-2. Also as depicted in FIG. 2, each capture probe typically includes a single sequence C-2 and thus hybridizes to a single capture extender. Optionally, however, a capture probe can include two or more sequences C-2 and hybridize to two or more capture extenders. Similarly, as depicted, each of the capture extenders in a particular set typically includes an identical sequence C-1, and thus only a single capture probe is needed for each set of particles; however, different capture extenders within a set optionally include different sequences C-1 (and thus hybridize to different sequences C-2, within a single capture probe or different capture probes on the surface of the corresponding set of particles).

One or more of the sets of particles is optionally isolated, whereby the associated target nucleic acid is isolated. The isolated nucleic acid can optionally be removed from the particles and/or subjected to further manipulation, if desired (e.g., amplification by PCR or the like).

Yet another exemplary embodiment is schematically illustrated in FIG. 3. This example demonstrates multiplex capture and detection of target nucleic acids, using a bDNA assay and a substantially planar solid support. Panel A depicts solid support 301 having nine capture probes provided on it at nine selected positions (e.g., 334-336). Panel B depicts a cross section of solid support 301, with distinct capture probes 304, 305, and 306 at different selected positions on the support (334, 335, and 336, respectively). A set of capture extenders is provided for each target nucleic acid. Only three sets are depicted; set 311 for nucleic acid 314, set 312 for nucleic acid 315 which is not present, and set 313 for nucleic acid 316. Each capture extender includes sequences C-1 (351, complementary to the respective capture probe's sequence C-2) and C-3 (352, complementary to a sequence in the corresponding target nucleic acid). Three sets of label extenders (321, 322, and 323 for nucleic acids 314, 315, and 316, respectively) and three sets of blocking probes (324, 325, and 326 for nucleic acids 314, 315, and 316, respectively) are also depicted (although nine would typically be provided, one for each nucleic acid of interest). Each label extender includes sequences L-1 (354, complementary to a sequence in the corresponding target nucleic acid) and L-2 (355, complementary to M-1).

A sample comprising whole blood is provided and the peripheral blood cells are lysed, producing a lysate (e.g., a whole blood lysate) including target nucleic acids 314 and 316; non-target nucleic acids 330 are also present in the lysate. Nucleic acids 314 and 316 are contacted with and hybridized to their corresponding set of capture extenders (311 and 313, respectively), and the capture extenders are hybridized to the corresponding capture probes (304 and 306, respectively), capturing nucleic acids 314 and 316 at selected positions 334 and 336, respectively (Panel C). Materials not bound to the solid support (e.g., capture extenders 312, nucleic acids 330, etc.) are optionally separated from the support by washing. Label probe system 340 including amplification multimer 341 (which includes sequences M-1 357 and M-2 358) and label probe 342 (which contains label 343) is hybridized to label extenders 321 and 323, which are hybridized to nucleic acids 314 and 316, respectively (Panel D). Materials not captured on the solid support are optionally removed by washing the support, and the presence or absence of the label at each position on the solid support is detected. Since each target nucleic acid is associated with a distinct selected position on the solid support via hybridization with the corresponding set of capture extenders and capture probe, the presence of the label at a given position on the solid support correlates with the presence of the corresponding target nucleic acid at that position and thus its presence in the original sample.

At any of various steps in the methods, materials not captured on the solid support are optionally separated from the support (and thus from any support-bound materials). For example, when detection is performed with a bDNA assay, after the capture extenders, nucleic acids, label extenders, blocking probes, and support-bound capture probes are hybridized, the solid support is optionally washed to remove unbound nucleic acids and probes; after the label extenders and amplification multimer are hybridized, the solid support is optionally washed to remove unbound amplification multimer; and/or after the label probes are hybridized to the amplification multimer, the solid support is optionally washed to remove unbound label probe prior to detection of the label.

The methods are optionally used to quantitate the amount of the first (and optional second, third, etc.) nucleic acid present in the whole blood sample. Thus, in one class of embodiments, detecting the presence of the first target nucleic acid on the solid support comprises detecting an amount of the first target nucleic acid on the solid support. It will be evident that the amount of the target nucleic acid captured on the solid support is proportional to the amount of the target nucleic acid present in the original sample. For example, in one class of embodiments in which a label is used, an intensity of a signal from the label can be measured (e.g., for each set of particles or each selected position on the solid support, in multiplex embodiments), and correlated with a quantity of the corresponding target nucleic acid present.

Due to efficient capture of each target nucleic acid by hybridization to multiple capture extenders, for example, even target nucleic acids present at low concentration can be captured and detected. Thus, in one class of embodiments, the first target nucleic acid is present in the sample in a non-zero amount of 100 amol or less, 50 amol or less, 10 amol or less, 1 amol or less, 0.1 amol or less, 0.05 amol or less, or even 0.01 amol or less. Similarly, two target nucleic acids can be captured and detected simultaneously, even when they differ greatly in concentration (e.g., by 1000-fold or more) in the sample. The methods are thus extremely versatile.

Capture of a particular target nucleic acid is optionally quantitative. Thus, in one exemplary class of embodiments, at least 30%, at least 50%, at least 80%, at least 90%, at least 95%, or even at least 99% of a total amount of the first target nucleic acid present in the sample is captured on the solid support. Second, third, etc. nucleic acids can similarly be quantitatively captured. Such quantitative capture can occur without capture of a significant amount of undesired nucleic acids, even those of very similar sequence to the target nucleic acid.

Thus, in one class of embodiments, in addition to the first target nucleic acid, the sample comprises or is suspected of comprising a nucleic acid which has a polynucleotide sequence which is 95% or more identical to that of the first target nucleic acid (e.g., 96% or more, 97% or more, 98% or more, or even 99% or more identical). The first target nucleic acid is captured on the solid support, while the other nucleic acid comprises 1% or less of a total amount of nucleic acid captured on the solid support (e.g., 0.5% or less, 0.2% or less, or even 0.1% or less; for multiplex embodiments, percent capture is assessed, e.g., on the corresponding first set of particles or first selected position on the solid support). The other nucleic acid can be another target nucleic acid or simply any nucleic acid. Typically, capture extenders are chosen that hybridize to regions of the first target nucleic acid having the greatest sequence difference from the other nucleic acid.

A capture probe and/or capture extender optionally comprises at least one non-natural nucleotide. For example, a capture probe and the corresponding capture extender optionally comprise, at complementary positions, at least one pair of non-natural nucleotides that base pair with each other but that do not Watson-Crick base pair with the bases typical to biological DNA or RNA (i.e., A, C, G, T, or U). Examples of nonnatural nucleotides include, but are not limited to, Locked NucleicAcid™ nucleotides (available from Exiqon A/S, www (dot) exiqon (dot) com; see, e.g., SantaLucia Jr. (1998) Proc Natl Acad Sci 95:1460-1465) and isoG, isoC, and other nucleotides used in the AEGIS system (Artificially Expanded Genetic Information System, available from EraGen Biosciences, www (dot) eragen (dot) com; see, e.g., U.S. Pat. No. 6,001,983, U.S. Pat. No. 6,037,120, and U.S. Pat. No. 6,140,496). Use of such non-natural base pairs (e.g., isoG-isoC base pairs) in the capture probes and capture extenders can, for example, reduce background and/or simplify probe design by decreasing cross hybridization, or it can permit use of shorter capture probes and capture extenders when the non-natural base pairs have higher binding affinities than do natural base pairs. Non-natural nucleotides can similarly be included in the label extenders, amplification multimers, and/or label probes, if desired.

Methods for Detecting Nucleic Acids from Plasma

Similar methods can be used to detect nucleic acids from blood plasma. Although current techniques typically involve concentration of RNA from large volumes of plasma prior to detection, e.g., by passing the plasma through a column to collect circulating RNAs on the column or by isolation of viral particles, the methods of the present invention facilitate detection of nucleic acids directly from the plasma.

Thus, one general class of embodiments provides methods of detecting at least a first target nucleic acid. In the methods, plasma comprising the first target nucleic acid is provided. The plasma is contacted with a first set of n capture extenders, wherein n is at least two. The first set of capture extenders is capable of hybridizing to the first target nucleic acid. The first target nucleic acid is hybridized to the first set of capture extenders, and the first set of capture extenders is associated with a solid support. The first target nucleic acid is captured on the solid support by hybridizing the first target nucleic acid to the first set of capture extenders and associating the first set of capture extenders with the solid support. The presence of the first target nucleic acid on the solid support is then detected. The hybridization and association steps can be, e.g., either simultaneous or sequential.

In one class of embodiments, the methods include contacting the plasma with an exogenously supplied protease (a protease that is added to the plasma by a user of the methods, as opposed to a protease which is endogenous to plasma and is thus already present), typically prior to contacting the plasma with the first set of capture extenders. As for the methods above, a variety of proteases are known in the art and can be adapted to the practice of the present invention; an effective concentration of protease, time for which the lysate is incubated with the protease, and the like can be determined by routine experimentation, e.g., by ensuring that an exogenously added RNA can be quantitatively detected in the plasma. In one embodiment, the protease is proteinase K.

The plasma is optionally contacted with the protease in a digestion mixture, and the volume of plasma in the mixture is optionally at most ½, at most ⅓, or at most ⅕ the volume of the mixture. For example, the volume of plasma used can be at most 1/10, 1/50, 1/100, or 1/150 the volume of the mixture. The remainder of the volume of the mixture can comprise a buffered salt solution, a detergent (e.g., lithium lauryl sulfate), water, and/or the like; for example, the plasma can be mixed with a lysis buffer such as that described in Example 1 below.

The methods can be applied to detection of essentially any type of nucleic acids. For example, the first target nucleic acid can be a DNA or an RNA. A target nucleic acid can, for example, be expressed by the organism from which the plasma is obtained or by a pathogen, and can be, e.g., free in the plasma or associated with one or more proteins, lipids, and/or the like, e.g. as a virion.

It will be understood that if the first target nucleic acid is initially present in the plasma in a double-stranded form, e.g., hybridized to a complementary nucleic acid, the double-stranded form is denatured prior to hybridizing the first target nucleic acid to the first set of capture extenders. Denaturation can be accomplished, for example, by thermal denaturation, exposure to alkaline conditions (which can have the added advantage of digesting extraneous RNA if the target nucleic acid is a DNA), or similar techniques. The methods can thus be used for detecting, e.g., double-stranded genomic DNA, double-stranded viral nucleic acids, and the like, as well as single-stranded nucleic acids such as mRNAs.

Essentially all of the features noted for the methods above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, type of solid support, association of the capture extenders with the solid support, detection technique, composition of the optional label probe system, type of label, inclusion of blocking probes, quantitation of the target nucleic acid(s), separation of unbound materials from the solid support, and/or the like.

For example, in one preferred class of embodiments, a first capture probe is bound to the solid support, and associating the first set of capture extenders with the solid support comprises hybridizing the capture extenders to the first capture probe. As another example, the presence of the first target nucleic acid on the solid support is optionally detected by hybridizing a first set of one or more label extenders and a label probe system comprising a label to the first target nucleic acid and then detecting the presence of the label on the solid support.

As for the embodiments above, the methods can be conveniently multiplexed to detect two or more target nucleic acids simultaneously. Thus, in one class of embodiments, the plasma comprises a second target nucleic acid and the methods include contacting the plasma with a second set of m capture extenders, wherein m is at least two (preferably at the same time the plasma is contacted with the first set of capture extenders); this second set of capture extenders is capable of hybridizing to the second target nucleic acid. The second target nucleic acid is hybridized to the second set of capture extenders, and the second set of capture extenders is associated with the solid support. Hybridizing the second target nucleic acid to the second set of capture extenders and associating the second set of capture extenders with the solid support captures the second target nucleic acid on the solid support. The presence of the second target nucleic acid on the solid support is then detected. It will be evident that n, the number of capture extenders in the first set, can but need not be the same as m, the number of capture extenders in the second set. As for the first target nucleic acid, the second target nucleic acid can be essentially any type of nucleic acid.

In one class of embodiments, the solid support is a substantially planar solid support, the first target nucleic acid is captured at a first selected position on the solid support, and the second target nucleic acid is captured at a second selected position on the solid support. For example, the first set of capture extenders can be hybridized to a first capture probe predisposed at the first selected position, while the second set of capture extenders is hybridized to a second capture probe predisposed at the second selected position. As for the embodiments above, essentially any suitable solid support can be employed.

In another class of embodiments, the solid support comprises a population of particles. The population includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first target nucleic acid is captured on a first set of the particles, and the second target nucleic acid is captured on a second set of the particles. For example, the first set of particles can comprise a first capture probe that is capable of hybridizing to the capture extenders comprising the first set of capture extenders (and thereby capturing the first target nucleic acid on the first set of particles), and the second set of particles can comprise a second capture probe that is capable of hybridizing to the capture extenders comprising the second set of capture extenders (and thereby capturing the second target nucleic acid on the second set of particles). In this class of embodiments, detecting the presence of the first and second nucleic acid on the solid support typically includes identifying at least a portion of the particles from each set and detecting the presence of nucleic acid on particles from each set. As for the embodiments above, essentially any suitable particles, e.g., particles having distinguishable characteristics and to which capture probes can be attached, can be used. For example, in one preferred class of embodiments, the particles are microspheres.

It will be evident that third, fourth, fifth, etc. target nucleic acids are optionally also detected. The at least one target nucleic acid to be detected thus optionally includes two or more, five or more, 10 or more, 20 or more, 30 or more, 40 or more, 50 or more, or even 100 or more target nucleic acids which are present or suspected to be present in the whole blood. A like number of sets of capture extenders, and typically a like number of selected positions on a substantially planar solid support or a like number of sets of particles, are also provided and used to capture and detect the target nucleic acids.

Compositions

Compositions related to the methods are another feature of the invention. Thus, one general class of embodiments provides a composition that includes a first set of n capture extenders, wherein n is at least two, and peripheral blood cell nucleic acids. The first set of capture extenders is capable of hybridizing to (and optionally is hybridized to) a first target nucleic acid. The first set of capture extenders is associated with, or is capable of being associated with, a solid support.

In one class of embodiments, the composition includes a whole blood lysate comprising the peripheral blood cell nucleic acids. The volume of whole blood from which the lysate is produced is optionally at most ½, ⅓, ⅕, 1/10, 1/50, 1/100, or 1/150 the volume of the composition. In another class of embodiments, the composition includes a peripheral blood cell lysate comprising the peripheral blood cell nucleic acids.

The composition can include the first target nucleic acid. The peripheral blood cell nucleic acids optionally comprise the first target nucleic acid; alternatively, the first target nucleic acid can, e.g., be a nucleic acid found in the plasma. The composition optionally includes nucleic acids from whole blood, where nucleic acids from plasma and all blood cell types (e.g., red blood cells, white blood cells, and platelets) are represented or potentially represented, no plasma, cells, or cell type having been deliberately enriched in or removed from the sample of whole blood.

In one class of embodiments, the composition includes an exogenously supplied protease (e.g., proteinase K) and/or a detergent. The composition optionally also includes reagents used to detect the first target nucleic acid. For example, in one class of embodiments, the composition includes a first set of one or more label extenders, which first set of label extenders is capable of hybridizing to (and optionally is hybridized to) the first target nucleic acid. The composition optionally also includes a label probe system comprising a label.

The composition can include the solid support. The capture extenders are optionally bound to the solid support, e.g., covalently or noncovalently, directly or through a linker, e.g., streptavidin-biotin or the like. In one preferred class of embodiments, a first capture probe is bound to the solid support. The first capture probe is capable of hybridizing to (and optionally is hybridized to) the capture extenders of the first set of capture extenders and thereby associating the capture extenders with the solid support. As noted above, the solid support can be essentially any suitable support, including any of a variety of materials, configurations, and the like. For example, in one class of embodiments, the solid support is a substantially planar solid support, e.g., an upper surface of the bottom of a well of a multiwell plate, a slide, or the like. Similarly, suitable solid supports include any surface of a well of a multiwell plate, whether planar or not. As another example, the solid support can comprise a plurality of particles, e.g., microspheres, beads, cylindrical particles, irregularly shaped particles, or the like. The particles are optionally identifiable, and optionally have additional or other desirable characteristics.

The composition optionally includes a second set of m capture extenders, wherein m is at least two. The second set of capture extenders is capable of hybridizing to (and optionally is hybridized to) a second target nucleic acid, and the second set of capture extenders is associated with, or is capable of being associated with, the solid support. In one class of embodiments, the solid support is a substantially planar solid support, wherein the first set of capture extenders is associated with or is capable of being associated with a first selected position on the solid support, and wherein the second set of capture extenders is associated with or is capable of being associated with a second selected position on the solid support. A first capture probe capable of hybridizing to the capture extenders of the first set is optionally bound to the solid support at the first selected position while a second capture probe capable of hybridizing to the capture extenders of the second set is bound to the solid support at the second selected position. In another class of embodiments, the solid support comprises a population of particles that includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first set of capture extenders is associated with or is capable of being associated with a first set of the particles, and the second set of capture extenders is associated with or is capable of being associated with a second set of the particles. Optionally, the first set of particles comprises a first capture probe capable of hybridizing to the capture extenders comprising the first set of capture extenders, while the second set of particles comprises a second capture probe capable of hybridizing to the capture extenders comprising the second set of capture extenders. The composition optionally includes the second target nucleic acid. It will be evident that the composition optionally also includes third, fourth, fifth, etc. target nucleic acids, sets of capture extenders, sets of particles or selected positions on the solid support, and/or the like.

Essentially all of the features noted for the methods above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, composition of the label probe system, type of label, inclusion of blocking probes, type of target nucleic acid(s), and/or the like.

Another general class of embodiments provides a composition that includes a first set of n capture extenders, wherein n is at least two, and plasma. The first set of capture extenders is capable of hybridizing to (and optionally is hybridized to) a first target nucleic acid. The first set of capture extenders is associated with, or is capable of being associated with, a solid support.

The composition can include the first target nucleic acid. In one class of embodiments, the composition includes an exogenously supplied protease (e.g., proteinase K) and/or a detergent. The volume of the plasma is optionally at most ½, ⅓, ⅕, 1/10, 1/50, 1/100, or 1/150 the volume of the composition. The composition optionally also includes reagents used to detect the first target nucleic acid. For example, in one class of embodiments, the composition includes a first set of one or more label extenders, which first set of label extenders is capable of hybridizing to the first target nucleic acid. The composition optionally also includes a label probe system comprising a label.

The composition can include the solid support. The capture extenders are optionally bound to the solid support, e.g., covalently or noncovalently, directly or through a linker, e.g., streptavidin-biotin or the like. In one preferred class of embodiments, a first capture probe is bound to the solid support. The first capture probe is capable of hybridizing to the capture extenders of the first set of capture extenders and thereby associating the capture extenders with the solid support. As noted above, the solid support can be essentially any suitable support, including any of a variety of materials, configurations, and the like. For example, in one class of embodiments, the solid support is a substantially planar solid support, e.g., an upper surface of the bottom of a well of a multiwell plate, a slide, or the like. Similarly, suitable solid supports include any surface of a well of a multiwell plate, whether planar or not. As another example, the solid support can comprise a plurality of particles, e.g., microspheres, beads, cylindrical particles, irregularly shaped particles, or the like. The particles are optionally identifiable, and optionally have additional or other desirable characteristics.

The composition optionally includes a second set of m capture extenders, wherein m is at least two. The second set of capture extenders is capable of hybridizing to (and optionally is hybridized to) a second target nucleic acid, and the second set of capture extenders is associated with, or is capable of being associated with, the solid support. In one class of embodiments, the solid support is a substantially planar solid support, wherein the first set of capture extenders is associated with or is capable of being associated with a first selected position on the solid support, and wherein the second set of capture extenders is associated with or is capable of being associated with a second selected position on the solid support. A first capture probe capable of hybridizing to the capture extenders of the first set is optionally bound to the solid support at the first selected position while a second capture probe capable of hybridizing to the capture extenders of the second set is bound to the solid support at the second selected position. In another class of embodiments, the solid support comprises a population of particles that includes at least two sets of particles, and the particles in each set are distinguishable from the particles in every other set. The first set of capture extenders is associated with or is capable of being associated with a first set of the particles, and the second set of capture extenders is associated with or is capable of being associated with a second set of the particles. Optionally, the first set of particles comprises a first capture probe capable of hybridizing to the capture extenders comprising the first set of capture extenders, while the second set of particles comprises a second capture probe capable of hybridizing to the capture extenders comprising the second set of capture extenders. The composition optionally includes the second target nucleic acid. It will be evident that the composition optionally also includes third, fourth, fifth, etc. target nucleic acids, sets of capture extenders, sets of particles or selected positions on the solid support, and/or the like.

Essentially all of the features noted for the embodiments above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, composition of the label probe system, type of label, inclusion of blocking probes, type of target nucleic acid(s), and/or the like.

Kits

Yet another general class of embodiments provides a kit for detecting at least a first target nucleic acid. The kit includes a first capture probe bound to a solid support, a first set of n capture extenders, wherein n is at least two, a label probe system comprising a label, a first set of one or more label extenders, a first solution comprising a detergent, a protease, and instructions for detecting the first target nucleic acid in whole blood, in peripheral blood cells, and/or in plasma with the kit, packaged in one or more containers. The first set of capture extenders is capable of hybridizing to the first target nucleic acid and to the first capture probe, and the label extenders of the first set are capable of hybridizing to the first target nucleic acid and to the label probe system.

The protease can be included in the first solution, provided in another solution, or provided in dried form, for example. The first solution typically includes a buffer, salt, and/or the like in addition to the detergent (e.g., a detergent such as lithium lauryl sulfate). The kit optionally also includes additional buffered solutions (e.g., diluent, hybridization buffer, and/or wash buffer), standards comprising one or more nucleic acids at known concentration, blocking probes, and/or the like.

In one aspect, the kits are configured for multiplex detection of target nucleic acids. Thus, in one class of embodiments, the kit also includes a second capture probe bound to the solid support, a second set of m capture extenders, wherein m is at least two, and a second set of one or more label extenders. The second set of capture extenders is capable of hybridizing to a second target nucleic acid and to the second capture probe, and the label extenders of the second set are capable of hybridizing to the second target nucleic acid and to the label probe system. It will be evident that third, fourth, fifth, etc. support-bound capture probes, sets of capture extenders, and sets of label extenders are optionally also included in the kit, for detection of third, fourth, fifth, etc. target nucleic acids.

Essentially all of the features noted for the embodiments above apply to these embodiments as well, as relevant; for example, with respect to number of capture extenders per set, type of solid support, association of the capture extenders with the solid support, composition of the label probe system, type of label, type of target nucleic acid(s), and/or the like.

Systems

In one aspect, the invention includes systems, e.g., systems used to practice the methods herein and/or comprising the compositions described herein. The system can include, e.g., a fluid and/or particle (e.g., microsphere) handling element, a fluid and/or particle containing element, a laser for exciting a fluorescent label and/or fluorescent particles, a detector for detecting light emissions from a chemiluminescent reaction or fluorescent emissions from a fluorescent label and/or fluorescent particles, and/or a robotic element that moves other components of the system from place to place as needed (e.g., a multiwell plate handling element). For example, in one class of embodiments, a composition of the invention is contained in a flow cytometer, a Luminex® 100™ or HTS™ instrument, a microplate reader, a microarray reader, a luminometer, a colorimeter, or like instrument.

The system can optionally include a computer. The computer can include appropriate software for receiving user instructions, either in the form of user input into a set of parameter fields, e.g., in a GUI, or in the form of preprogrammed instructions, e.g., preprogrammed for a variety of different specific operations. The software optionally converts these instructions to appropriate language for controlling the operation of components of the system (e.g., for controlling a fluid handling element, robotic element and/or laser). The computer can also receive data from other components of the system, e.g., from a detector, and can interpret the data, provide it to a user in a human readable format, or use that data to initiate further operations, in accordance with any programming by the user.

Labels

A wide variety of labels are well known in the art and can be adapted to the practice of the present invention. For example, luminescent labels and light-scattering labels (e.g., colloidal gold particles) have been described. See, e.g., Csaki et al. (2002) “Gold nanoparticles as novel label for DNA diagnostics” Expert Rev Mol Diagn 2:187-93.

As another example, a number of fluorescent labels are well known in the art, including but not limited to, hydrophobic fluorophores (e.g., phycoerythrin, rhodamine, Alexa Fluor 488 and fluorescein), green fluorescent protein (GFP) and variants thereof (e.g., cyan fluorescent protein and yellow fluorescent protein), and quantum dots. See e.g., Haughland (2003) Handbook of Fluorescent Probes and Research Products, Ninth Edition or Web Edition, from Molecular Probes, Inc., for descriptions of fluorophores emitting at various different wavelengths (including tandem conjugates of fluorophores that can facilitate simultaneous excitation and detection of multiple labeled species). For use of quantum dots as labels for biomolecules, see e.g., Dubertret et al. (2002) Science 298:1759; Nature Biotechnology (2003) 21:41-46; and Nature Biotechnology (2003) 21:47-51.

Labels can be introduced to molecules, e.g. polynucleotides, during synthesis or by postsynthetic reactions by techniques established in the art; for example, kits for fluorescently labeling polynucleotides with various fluorophores are available from Molecular Probes, Inc. (www (dot) molecularprobes (dot) com), and fluorophore-containing phosphoramidites for use in nucleic acid synthesis are commercially available. Similarly, signals from the labels (e.g., absorption by and/or fluorescent emission from a fluorescent label) can be detected by essentially any method known in the art. For example, multicolor detection, detection of FRET, fluorescence polarization, and the like, are well known in the art.

Microspheres

Microspheres are preferred particles in certain embodiments described herein since they are generally stable, are widely available in a range of materials, surface chemistries and uniform sizes, and can be fluorescently dyed. Microspheres can be distinguished from each other by identifying characteristics such as their size (diameter) and/or their fluorescent emission spectra, for example.

Luminex Corporation (www (dot) luminexcorp (dot) com), for example, offers 100 sets of uniform diameter polystyrene microspheres. The microspheres of each set are internally labeled with a distinct ratio of two fluorophores. A flow cytometer or other suitable instrument can thus be used to classify each individual microsphere according to its predefined fluorescent emission ratio. Fluorescently-coded microsphere sets are also available from a number of other suppliers, including Radix Biosolutions (www (dot) radixbiosolutions (dot) com) and Upstate Biotechnology (www (dot) upstatebiotech (dot) com). Alternatively, BD Biosciences (www (dot) bd (dot) com) and Bangs Laboratories, Inc. (www (dot) bangslabs (dot) com) offer microsphere sets distinguishable by a combination of fluorescence and size. As another example, microspheres can be distinguished on the basis of size alone, but fewer sets of such microspheres can be multiplexed in an assay because aggregates of smaller microspheres can be difficult to distinguish from larger microspheres.

Microspheres with a variety of surface chemistries are commercially available, from the above suppliers and others (e.g., see additional suppliers listed in Kellar and Iannone (2002) “Multiplexed microsphere-based flow cytometric assays” Experimental Hematology 30:1227-1237 and Fitzgerald (2001) “Assays by the score” The Scientist 15[11]:25). For example, microspheres with carboxyl, hydrazide or maleimide groups are available and permit covalent coupling of molecules (e.g., polynucleotide capture probes with free amine, carboxyl, aldehyde, sulfhydryl or other reactive groups) to the microspheres. As another example, microspheres with surface avidin or streptavidin are available and can bind biotinylated capture probes; similarly, microspheres coated with biotin are available for binding capture probes conjugated to avidin or streptavidin. In addition, services that couple a capture reagent of the customer's choice to microspheres are commercially available, e.g., from Radix Biosolutions (www (dot) radixbiosolutions (dot) com).

Protocols for using such commercially available microspheres (e.g., methods of covalently coupling polynucleotides to carboxylated microspheres for use as capture probes, methods of blocking reactive sites on the microsphere surface that are not occupied by the polynucleotides, methods of binding biotinylated polynucleotides to avidin-functionalized microspheres, and the like) are typically supplied with the microspheres and are readily utilized and/or adapted by one of skill. In addition, coupling of reagents to microspheres is well described in the literature. For example, see Yang et al. (2001) “BADGE, Beads Array for the Detection of Gene Expression, a high-throughput diagnostic bioassay” Genome Res. 11:1888-98; Fulton et al. (1997) “Advanced multiplexed analysis with the FlowMetrix™ system” Clinical Chemistry 43:1749-1756; Jones et al. (2002) “Multiplex assay for detection of strain-specific antibodies against the two variable regions of the G protein of respiratory syncytial virus” 9:633-638; Camilla et al. (2001) “Flow cytometric microsphere-based immunoassay: Analysis of secreted cytokines in whole-blood samples from asthmatics” Clinical and Diagnostic Laboratory Immunology 8:776-784; Martins (2002) “Development of internal controls for the Luminex instrument as part of a multiplexed seven-analyte viral respiratory antibody profile” Clinical and Diagnostic Laboratory Immunology 9:41-45; Kellar and Iannone (2002) “Multiplexed microsphere-based flow cytometric assays” Experimental Hematology 30:1227-1237; Oliver et al. (1998) “Multiplexed analysis of human cytokines by use of the FlowMetrix system” Clinical Chemistry 44:2057-2060; Gordon and McDade (1997) “Multiplexed quantification of human IgG, IgA, and IgM with the FlowMetrix™ system” Clinical Chemistry 43:1799-1801; U.S. Pat. No. 5,981,180 entitled “Multiplexed analysis of clinical specimens apparatus and methods” to Chandler et al. (Nov. 9, 1999); U.S. Pat. No. 6,449,562 entitled “Multiplexed analysis of clinical specimens apparatus and methods” to Chandler et al. (Sep. 10, 2002); and references therein.

Methods of analyzing microsphere populations (e.g. methods of identifying microsphere subsets by their size and/or fluorescence characteristics, methods of using size to distinguish microsphere aggregates from single uniformly sized microspheres and eliminate aggregates from the analysis, methods of detecting the presence or absence of a fluorescent label on the microsphere subset, and the like) are also well described in the literature. See, e.g., the above references.

Suitable instruments, software, and the like for analyzing microsphere populations to distinguish subsets of microspheres and to detect the presence or absence of a label (e.g., a fluorescently labeled label probe) on each subset are commercially available. For example, flow cytometers are widely available, e.g., from Becton-Dickinson (www (dot) bd (dot) com) and Beckman Coulter (www (dot) beckman (dot) com). Luminex® 100™ and Luminex HTS™ systems (which use microfluidics to align the microspheres and two lasers to excite the microspheres and the label) are available from Luminex Corporation (www (dot) luminexcorp (dot) com); the similar Bio-Plex™ Protein Array System is available from Bio-Rad Laboratories, Inc. (www (dot) bio-rad (dot) com). A confocal microplate reader suitable for microsphere analysis, the FMAT™ System 8100, is available from Applied Biosystems (www (dot) appliedbiosystems (dot) com).

As another example of particles that can be adapted for use in the present invention, sets of microbeads that include optical barcodes are available from CyVera, now part of Illumina, Inc. (www (dot) illumina (dot) com). The optical barcodes are holographically inscribed digital codes that diffract a laser beam incident on the particles, producing an optical signature unique for each set of microbeads.

Molecular Biological Techniques

In practicing the present invention, many conventional techniques in molecular biology, microbiology, and recombinant DNA technology are optionally used. These techniques are well known and are explained in, for example, Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif.; Sambrook et al., Molecular Cloning—A Laboratory Manual (3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2000 and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2005). Other useful references, e.g. for cell isolation and culture (e.g., for subsequent nucleic acid or protein isolation) include Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New York and the references cited therein; Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips (Eds.) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg New York) and Atlas and Parks (Eds.) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, Fla.

Making Polynucleotides

Methods of making nucleic acids (e.g., by in vitro amplification, purification from cells, or chemical synthesis), methods for manipulating nucleic acids (e.g., by restriction enzyme digestion, ligation, etc.) and various vectors, cell lines and the like useful in manipulating and making nucleic acids are described in the above references. In addition, methods of making branched polynucleotides (e.g., amplification multimers) are described in U.S. Pat. No. 5,635,352, U.S. Pat. No. 5,124,246, U.S. Pat. No. 5,710,264, and U.S. Pat. No. 5,849,481, as well as in other references mentioned above.

In addition, essentially any polynucleotide (including, e.g., labeled or biotinylated polynucleotides) can be custom or standard ordered from any of a variety of commercial sources, such as The Midland Certified Reagent Company (www (dot) mcrc (dot) com), The Great American Gene Company (www (dot) genco (dot) com), ExpressGen Inc. (www (dot) expressgen (dot) com), Qiagen (on the internet at oligos (dot) qiagen (dot) com) and many others.

A label, biotin, or other moiety can optionally be introduced to a polynucleotide, either during or after synthesis. For example, a biotin phosphoramidite can be incorporated during chemical synthesis of a polynucleotide. Alternatively, any nucleic acid can be biotinylated using techniques known in the art; suitable reagents are commercially available, e.g., from Pierce Biotechnology (www (dot) piercenet (dot) com). Similarly, any nucleic acid can be fluorescently labeled, for example, by using commercially available kits such as those from Molecular Probes, Inc. (www (dot) molecularprobes (dot) com) or Pierce Biotechnology (www (dot) piercenet (dot) com) or by incorporating a fluorescently labeled phosphoramidite during chemical synthesis of a polynucleotide.

Arrays

In an array of capture probes on a solid support (e.g., a membrane, a glass or plastic slide, a silicon or quartz chip, a plate, or other spatially addressable solid support), each capture probe is typically bound (e.g., electrostatically or covalently bound, directly or via a linker) to the support at a unique selected location. Methods of making, using, and analyzing such arrays (e.g., microarrays) are well known in the art. See, e.g., Baldi et al. (2002) DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Cambridge University Press; Beaucage (2001) “Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications” Curr Med Chem 8:1213-1244; Schena, ed. (2000) Microarray Biochip Technology, pp. 19-38, Eaton Publishing; technical note “Agilent SurePrint Technology: Content centered microarray design enabling speed and flexibility” available at www (dot) chem (dot) agilent (dot) com/temp/rad01539/00039489 (dot) pdf; and references therein. Arrays of pre-synthesized polynucleotides can be formed (e.g., printed), for example, using commercially available instruments such as a GMS 417 Arrayer (Affymetrix, Santa Clara, Calif.). Alternatively, the polynucleotides can be synthesized at the selected positions on the solid support; see, e.g., U.S. Pat. No. 6,852,490 and U.S. Pat. No. 6,306,643, each to Gentanlen and Chee entitled “Methods of using an array of pooled probes in genetic analysis.”

Suitable solid supports are commercially readily available. For example, a variety of membranes (e.g., nylon, PVDF, and nitrocellulose membranes) are commercially available, e.g., from Sigma-Aldrich, Inc. www (dot) sigmaaldrich (dot) com). As another example, surface-modified and pre-coated slides with a variety of surface chemistries are commercially available, e.g., from TeleChem International (www (dot) arrayit (dot) com), Corning, Inc. (Corning, N.Y.), or Greiner Bio-One, Inc. (www (dot) greinerbiooneinc (dot) com). For example, silanated and silyated slides with free amino and aldehyde groups, respectively, are available and permit covalent coupling of molecules (e.g., polynucleotides with free aldehyde, amine, or other reactive groups) to the slides. As another example, slides with surface streptavidin are available and can bind biotinylated capture probes. In addition, services that produce arrays of polynucleotides of the customer's choice are commercially available, e.g., from TeleChem International (www (dot) arrayit (dot) com) and Agilent Technologies (Palo Alto, Calif.).

Suitable instruments, software, and the like for analyzing arrays to distinguish selected positions on the solid support and to detect the presence or absence of a label (e.g., a fluorescently labeled label probe) at each position are commercially available. For example, microarray readers are available, e.g., from Agilent Technologies (Palo Alto, Calif.), Affymetrix (Santa Clara, Calif.), and Zeptosens (Switzerland).

EXAMPLES

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. Accordingly, the following examples are offered to illustrate, but not to limit, the claimed invention.

Example 1 Sensitive and Quantitative Measurement of Gene Expression Directly from Peripheral Whole Blood

The following sets forth a series of experiments that demonstrate detection of nucleic acids from whole blood using bDNA assays. Both singleplex and multiplex assays are described.

Using current techniques, gene expression analysis of whole blood requires cell isolation, RNA purification, and/or target amplification. This example, however, describes an assay to measure single- or multiplexed gene expression directly from whole blood without RNA purification, labeling, or amplification. The assay can detect, e.g., as little as 0.01 attomol (singleplex) or 0.04 attomol (multiplex) of a target mRNA in 30 μl of blood, with a coefficient of variation less than 10% and a dynamic range of 3-4 logs. The assay is sensitive enough to quantitatively measure gene expression from cells in the minority in whole blood, with signals that are several times higher than those from assays using RNA purified from an equivalent amount of blood. The assay was used to evaluate the impact of blood processing on gene expression and indicated that PAXgene® treatment induced expression of known antiapoptotic genes during processing of the whole blood.

The method can directly measure RNA in whole blood lysates, with excellent sensitivity and reproducibility. The assay does not require blood processing (other than direct lysis), RNA extraction, or enzymatic manipulation of sample RNA. Because detection is based on hybridization between a target RNA and oligonucleotide probes, no enzymatic manipulation of the target is needed; the measured signal is directly proportional to the target RNA, instead of to any derivatives of it such as cDNA, cRNA, or an amplified product. The assay is presented in a singleplex format using a multi-well plate and chemiluminescent detection, and in a multiplex format combining the Luminex xMAP® encoded bead platform with fluorescent detection.

Overview of the Assay

Analogous to an ELISA sandwich assay, this exemplary assay utilizes nucleic acid sandwich binding to capture target RNAs in whole blood lysates to a solid support. The ability to quantify an mRNA transcript without target labeling lies in the design of a set of target-specific oligonucleotide probes (e.g., about 20 probes per target as in this example). The detection signal is amplified using branched-DNA (bDNA) signal amplification technology (Urdea, M. S. et al. (1991) “Branched DNA amplification multimers for the sensitive: direct detection of human hepatitis viruses” Nucleic Acids Symp Ser 24:197-200). An overview of the assay is shown in FIG. 1.

Assay Performance

bDNA assays have been used successfully to quantify gene expression in total RNA and tissue culture lysates and in viral particles purified from human plasma (Urdea, M. S. et al. (1991) “Branched DNA amplification multimers for the sensitive:direct detection of human hepatitis viruses” Nucleic Acids Symp Ser 24:197-200; Hartley, D. P. and Klaassen, C. D. (2000) “Detection of Chemical-Induced Differential Expression of Rat Hepatic Cytochrome P450 mRNA Transcripts Using Branched DNA Signal Amplification Technology” Drug Metab Dispos 28:608-616; Wang, J. et al. (1997) Regulation of insulin preRNA splicing by glucose” PNAS 94:4360-4365; and Gleaves, C. A. et al. (2002) “Multicenter evaluation of the Bayer VERSANT HIV-1 RNA 3.0 assay: analytical and clinical performance” J Clin Virol 25:205-16). However, there has been no report on the use of bDNA to directly detect RNA in whole blood, presumably because of the unique challenges presented by whole blood that are not found in other tissues or cultured cells, including high protein content from plasma and red cells and high ribonuclease activity. Initial attempts to apply bDNA technology to measurement of mRNA from whole blood failed to generate specific signals. The complex content in blood lysates resulted in nonspecific binding of probes and high background, and the addition of blood lysate into purified in vitro transcripts resulted in significant loss of transcript signals, suggesting the presence of residual ribonuclease activity in the whole blood lysate.

However, the methods described herein, which include incubating the lysate with an effective concentration of protease for an effective time at an effective temperature and limiting the blood to lysis buffer ratio, can enable detection of mRNA from whole blood. Using these methods, a linear signal response was observed for GAPDH (FIG. 4 Panel A, diamonds; R²=0.9898) and other genes tested in 1-30 μl of whole blood, as well as in solubilized RNA pellets formed from equivalent amounts of whole blood stabilized in PAXgene® (FIG. 4 Panel B; R²=0.9927). The average coefficient of variation was 7% (representing 16 sample measurements, each in triplicate) with a range of 0.4%-16%.

It is important to note that although both RNA and genomic DNA are present in the blood lysate, only RNA hybridizes to the probes under the assay conditions, since the genomic DNAs apparently remain annealed. Probes complementary to the antisense strand of a target gene did not give significant signal from whole blood lysate under standard assay conditions (FIG. 4 Panel A, squares). In a separate experiment, 500 ng of purified human genomic DNA (equivalent to DNA from 20 μl whole blood) was hybridized with GAPDH probes under standard assay conditions, and no specific hybridization signals could be detected.

Known amounts of an exogenous E. coli transcript (dapB, which does not cross hybridize with any known mammalian RNA) were added to the whole blood lysate to assess the assay's analytical sensitivity. An in vitro E. coli dapB transcript was serially diluted, added to lysate produced from 30 μl whole blood, and quantitated using dapB specific probes. As shown in FIG. 4 Panel C, the assay can specifically detect as little as 6000 copies (0.01 attomole) of target in the background of 30 μl blood, which includes about 2×10⁵ white blood cells and 1.5×10⁸ red blood cells. Linear regression R² values for both curves are 0.99, and all signals are above the indicated Limit of Detection (LOD). The complex components in blood lysate do not interfere with the detection of the specific mRNA target. Nearly 100% of the target molecules were captured onto the solid surface, as indicated by the generation of only minimal signals in a second assay measuring the amount of target remaining in the unbound supernatant of the first assay. The dynamic range of this method spans 4 logs. Importantly, at all concentrations tested, target signals in the absence or presence of blood lysate are essentially identical (FIG. 4 Panel C). A similar result was obtained by adding transcripts of IL2, which was not detectable in unstimulated whole blood. These results indicate that this method permits specific quantitation of RNA, avoiding interference by blood constituents such as blood proteins and the high concentration of reticulocyte-specific RNAs such as globin.

To obtain a practical sense of the assay sensitivity, mRNAs of several blood cell surface markers were assayed in singleplex in 30 μl fresh whole blood (Table 1). mRNAs from all major blood subtypes in normal blood can be detected, including the minority cell types (e.g., B cells and NK cells). Thus, this assay provides the means to directly monitor gene expression in subpopulations of blood cells without blood fractionation.

TABLE 1 Detection of cell-type specific mRNA in whole blood. platelet platelet T cell T cell NK cell B cell Monocyte (reticulated) (reticulated) Approx. cell number per μl 1600 1600 300 300 500 9200 9200 mRNA CD3E CD5 CD56 CD19 CD14 CD61 CD41 30 μl Blood(SD)* 7.0(1.1) 3.0(0.3) 1.5(0.1) 1.7(0.2) 21.8(1.1)  11.1(1.9)  5.3(0.6) Control(SD)*, **  0.4(0.02)  0.3(0.01)  0.5(0.03)  0.3(0.03)  0.4(0.06)  0.5(0.06)  0.4(0.05) *units are RLUs **no blood

A multiplexed assay for simultaneous detection of multiple messages in whole blood was also developed. The assay exploits Luminex encoded-bead technology and flow cytometry. As schematically depicted in FIG. 5 Panel A, fluorescently distinguishable latex beads (426, 427, and 428) were conjugated with distinctive capture probe sequences (421, 422, and 423), pooled, and added to the assay well. Whole blood or PAXgene®-treated blood was lysed to release target mRNAs (411, 412, and 413), which bind to their respective capture extender (CE; e.g., 401, 402, and 403), label extender (LE; e.g., 406, 407, and 408), and blocking probe (BP; 410) probes. The CEs for different genes of interest carry distinctive extender sequences, each of which is complementary to the capture probe on the respective set of beads. After hybridization to capture the target on beads, bDNA amplifier molecules (430) were added and hybridized to the universal LE extender on each target, and biotinylated label probe oligos (431) were added to bind to the branches of the amplifier molecule (FIG. 5 Panel B). Strepavidin-conjugated phycoerythrin (SAPE; 432) was added to bind to the biotin on the label probes (FIG. 5 Panel C), and the beads were assayed by flow cytometry (e.g., on the Luminex® 100™ IS flow system). The characteristic intrinsic fluorescence color code of each bead (which is spectrally distinct from the SAPE fluorescence) identifies the target gene being assayed, and the SAPE fluorescence intensity on the bead measures the target concentration. The current capability of the Luminex platform (100 sets of distinctively coded beads) allows for up to 100 genes to be simultaneously assayed with this technology.

Experiments with added in vitro transcripts, in which a mixture of 9 target IVTs was serially diluted, added to lysate produced from 20 μl whole blood, and assayed using the multiplexed bead assay, indicated a good linearity of response (FIG. 6 Panel A) as well as high specificity (FIG. 6 Panel B). As shown in FIG. 6 Panel B, components of the whole blood lysate do not interfere with the specific detection of mRNA target. The multiplexed assay as described in this example has a detection limit of 0.04 amol (25,000 copies) of each target molecule per assay of lysate produced from 20 μl of blood (which can be lowered, e.g., by use of more LEs per target) (FIG. 6 Panel B), with an average coefficient of variation of 8.1%. The reduced sensitivity compared to the singleplex assay (FIG. 4 Panel C) resulted in part from the use of fluorescence detection instead of the more sensitive chemiluminescence detection.

The assay was validated by demonstrating the upregulation of inflammatory cytokine genes in whole blood in response to E. coli LPS stimulation. As determined by a 9-plex bead assay, after a 2 hour incubation of fresh whole blood at 37° C. with 10 μg/ml LPS, expression of IL-1beta, IL8, IL6, and TNF-alpha were significantly induced, while expression of IL2, IL10 and GM-CSF (CSF2) remains stable during this period (FIG. 6 Panel C), consistent with previously reported measurements of cytokine proteins (De Groote, D. et al. (1992) “Direct stimulation of cytokines (IL-1 beta, TNF-alpha, IL-6, IL-2, IFN-gamma and GM-CSF) in whole blood. I. Comparison with isolated PBMC stimulation” Cytokine 4:239-48). Signals are linear with increasing blood volume, and were detected even in the lowest volume (4 μl) tested (FIG. 6 Panels F and G). Interestingly, 37° C. ex vivo incubation alone (no LPS) caused significant basal induction of IL1b, IL8 and TNF-alpha, but not IL6, in whole blood (FIG. 6 Panel C), consistent with the sensitivity to environmental conditions whole blood displays. In contrast to the rapid response of inflammatory cytokine producing cells, the acquired immune response in whole blood was scarcely activated by LPS within 2 hours, as indicated by the lack of induction of several genes associated with antigen presenting cell activation (FIG. 6 Panel D); only ICAM1 showed significant induction. Results from the multiplex and singleplex platforms are highly consistent (FIG. 6 Panel E).

Assessment of the Effect of Blood Handling on Gene Expression

The assay having been demonstrated to represent a sensitive and quantitative method to directly assay blood RNA expression relatively free of biases, it was used to assess the impact of common pre-analytical blood handling procedures on gene expression. Similar attempts could previously only assess the combined impact from blood handling, RNA extraction, and post-extraction processing. A panel of about 30 genes including cytokines and apoptosis related genes was used to assess the blood state, since these genes are among the most sensitive to stress during ex vivo incubation (Baechler, E. C. et al. (2004) “Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation” Genes Immun 5:347-53). Identical blood samples were processed by red blood cell lysis, by Ficoll-Hipaque centrifugation (PBMC), by phenol/chloroform extraction of whole blood RNA, and by blood stabilization using the PAXgene® reagent. These processed blood samples (or RNA) were then lysed and assayed together with unprocessed whole blood lysates. The correlation coefficients of gene expression patterns between unprocessed and various processed blood samples are presented in Table 2.

TABLE 2 Correlation of the expression pattern of a panel of 26 genes between whole blood and processed blood. RBC- R square WB lys* PaxPellet WB RNA PaxRNA PBMC* WB 1 0.998 0.87 0.96 0.86 0.95 RBC-lys* 1 0.85 0.99 0.88 0.95 PaxPellet 1 0.93 0.84 0.82 WB RNA 1 0.77 0.93 PaxRNA 1 0.84 PBMC* 1 *Excluding BCL-XL Gene expression was determined by the multiplex assay described. Samples assayed are the following: WB: Fresh whole blood lysate. RBC-lys: Lysate of blood that underwent selective red cell lysis and was washed. PaxPellet: Solubilized PAXgene ® blood pellet. WB RNA: Whole blood RNA purified by phenol/chloroform extraction. RNA from 8x equivalent volume of blood was used. PaxRNA: RNA purified from PAXgene ® blood using recommended protocol. RNA from 10x equivalent volume of blood was 3used. PBMC: Lysate of peripheral blood mononuclear cells. List of genes assayed was the same as for FIG. 7 Panel A.

FIG. 7 Panel A depicts a graph illustrating correlation of the gene expression pattern in whole blood and red blood cell (RBC)-lysed blood. Lysates from 20 μl of whole blood and an equivalent volume of RBC-lysed blood were assayed in multiplex for expression of IL2, TNFa, IL10, IL6, IL1B, IFNg, IL8, CSF2, GAPDH, RELB, A20, CDKN1, NFKB1, NFKB2, RELA, NFKBIA, BAK, FASL, FAS, RAFTK, BAD, BCL-2, IL6R, BCL-XL, ACTB and CFLAR as described herein. The lysis of red blood cells resulted in little change in expression of the genes assayed, except for a significant reduction in expression of BCL-XL, a gene expressed in erythrocytes and having an important antiapoptotic role during erythropoiesis (Gregoli, P. A. and Bondurant, M. C. (1997) “The Roles of Bcl-XL and Apopain in the Control of Erythropoiesis by Erythropoietin” Blood 90:630-640). Linear regression (with BCL-XL excluded) showed good correlation in expression pattern; excluding BCL-XL, signals from genes in the panel show a strong correlation between whole blood and red blood cell lysed whole blood (R²=0.998, Table 2 and FIG. 7 Panel A). Ficoll centrifugation for PBMC resulted in changes in blood cell composition and not unexpectedly, the correlation with whole blood expression was lower (R²=0.95, Table 2).

When expression signals from whole blood lysates are compared with phenol/chloroform-purified total RNA, correlation is generally good except for some genes with low expression, where measurement precision is expectedly reduced (R²=0.96, Table 2 and FIG. 7 Panel B). However, the signals from direct lysates are 2-10 times stronger than the signals from purified RNA, depending on RNA extraction efficiency. The reduced signal in purified RNA appeared to be due to RNA loss during the purification procedure, since after normalization against an exogenous transcript spiked into the lysate before RNA extraction, the signals are equivalent. To produce the graph shown in FIG. 7 Panel B, lysates of whole blood (20 μl) and RNA extracted from whole blood were assayed in multiplex for expression of the genes listed for FIG. 7 Panel A. RNA equivalent to 160 μl whole blood was assayed to yield sufficient signals for most genes. Linear regression generates a straight line with slope of 2.34, significantly lower than the expected slope of 8, indicating that RNA extraction resulted in significant RNA loss.

Lysates from 20 μl of whole blood as well as from a pellet formed in an equivalent amount of whole blood stabilized at room temperature overnight in PAXgene® reagent were assayed in multiplex for expression of genes listed for FIG. 7 Panel A. PAXgene® caused significant changes in gene expression compared to direct whole blood measurement (Table 2 and FIG. 7 Panel C; R²=0.8759). Twenty microliters of whole blood and PAXgene® stabilized blood were assayed in singleplex format in the same plate; signals were normalized to GAPDH (FIG. 7 Panel D). The apoptosis genes such as CFLAR are particularly sensitive to PAXgene® reagent treatment (FIG. 7 Panel D), although their signals are comparable among direct lysate, purified RNA, and other processed blood samples. When CFLAR data was removed, the correlation significantly improved (R²=0.95 for PAXgene® pellet and R²=0.94 for PAXgene® purified RNA). As expected, the correlation became poorer as more handling steps were involved with any one sample. The lowest correlation resulted when comparing RNA purified from whole blood and RNA purified from PAXgene® stabilized blood (R²=0.77, Table 2).

Advantages

In contrast to microarray or RT-PCR analysis, which, e.g., rely on single probe-target interactions for target capture or detection, this exemplary assay used on average 20 probes, hybridizing to 500-600 contiguous bases of one target sequence. The multiple probe per target design offers significantly improved sensitivity and reproducibility for the assay. In addition to the benefit that multiple LE reporters are bound to one target, the assay optionally takes advantage of the fact that the interactions between contiguous probes and a target result in stronger, more stable helix formation due to base stacking effects (Dimitrov, R. A. and Zuker, M. (2004) “Prediction of Hybridization and Melting for Double-Stranded Nucleic Acids” Biophys. J. 87:215-226). The multidentate interaction between the solid surface and the many CEs bound to one target also ensures more robust and reproducible target capture. Finally, use of multiple probes minimizes the impact of the design of individual probes on signal, reducing assay variations. As a result the target capture efficiency in the singleplex plate assay approaches 100%, and the average CV (coefficient of variance) of this assay from replicate blood samples is routinely below 10%. In comparison, the CV from replicate blood samples in microarray analysis is 37% (Feezor, R. J. et al. (2004) “Whole blood and leukocyte RNA isolation for gene expression analyses” Physiol. Genomics 19:247-254), and for Taqman RT-PCR the CV for copy numbers is around 16% (Rainen et al., supra).

Another important benefit afforded by the multi-probe per target design is high specificity. Unlike in traditional microarray experiments, the high concentration of globin RNAs does not interfere with the assay. The bDNA assay requires both CEs and LEs to bind to the same RNA molecule in order for the RNA to give a signal, and multiple CEs typically have to bind to the same RNA target in order for the RNA to be captured on the solid surface, since the interaction between a single CE and a surface capture probe is optionally thermodynamically unstable at the assay hybridization temperature.

This assay can be used for quantitation of absolute gene expression by incorporating standard curves with known amounts of in vitro transcripts for each gene of interest. It is superior to quantitative RT-PCR for several reasons, including: 1) curves generated are linear, not logarithmic, 2) the product measured represents the actual amount of a given transcript, 3) hybridization efficiency is the same for samples and standards (FIG. 4 Panel C), whereas in RT-PCR amplification efficiency may not be the same, 4) results can be meaningfully expressed as copies per unit blood, not copies per unit RNA purified or copies relative to a unit housekeeper copy number, and 5) the assay can be conveniently multiplexed.

An important and unique advantage of this assay is its accurate result, free of biases from blood cell and RNA isolation procedures. The processing of clinical specimens such as peripheral blood samples is rarely ideal. The results with a panel of cytokine and apoptosis genes presented herein show that impact to expression pattern increases with increases in the number of processing steps, including RNA purification. Although PAXgene® may stabilize the expression pattern of some genes, the use of PAXgene® may result in invalid RNA quantitation for other genes, including certain apoptosis related genes such as CFLAR. Induction of selected genes by PAXgene® stabilization was also observed on human bone marrow aspirates (Breit, S. et al. I (2004) “Impact of pre-analytical handling on bone marrow mRNA gene expression” Br J Haematol 126:231-43). For biomarker discovery study using PAXgene® stabilized blood samples, especially if CFLAR is identified as one of the biomarkers (Horwitz, P. A. et al. (2004) “Detection of Cardiac Allograft Rejection and Response to Immunosuppressive Therapy With Peripheral Blood Gene Expression” Circulation 110:3815-3821), it is prudent to validate the markers using blood without PAXgene® treatment.

Blood biomarker studies often involve microarray profiling on a limited number of samples, followed by clinical validation of dozens of genes in a larger number of independent samples. The multiplexed bead assay described herein is well suited for the validation workflow, with its medium gene throughput and the high sample throughput capability. With proper probe design, the assay can be adapted to high multiplex formats such as microarrays and used in high throughput applications such as expression profiling of whole blood, without the need to purify, label, and amplify the RNA targets. The methods of the invention thus remove the most significant roadblock to the broader application of expression profiling in clinical applications.

The assays of the invention can significantly simplify clinical expression analysis. Blood drawn from, e.g., an ear bleed may be sufficient for some expression analyses. Similarly, RNA analysis can now be performed for infants or patients where only limited amounts of blood are available. The absence of the RNA purification requirement is especially useful for large-scale studies where sample analysis throughput has been limited by laborious RNA purification. The exceptional accuracy, consistency of the results, and the time saved in sample preparation and data analysis are significant advantages of these assays when compared with other assays for blood gene expression.

As described above, the methods of the invention can be used, for example, to detect target nucleic acid(s) from peripheral blood cells lysed in liquid whole blood. As another example, the methods can also be used to detect target nucleic acid(s) from a blood sample that is applied to a matrix (e.g., filter paper) and dried. The dried blood spot is contacted with blood lysis buffer (such as that described below) to lyse the peripheral blood cells (if necessary) and to elute the nucleic acid(s) from the filter paper or other matrix. The nucleic acid(s) in the resulting lysate are then hybridized to CE, LE, and BP sets and detected in singleplex or multiplex assays as described. The methods are similarly applicable to detection of target nucleic acids from plasma (e.g., liquid plasma or plasma dried on a matrix).

Experimental Protocol

Singleplex Assay for Whole Blood

Fresh, anticoagulated blood (with EDTA, heparin, or citrate as the anticoagulant) from healthy donors (Stanford Blood Center, Stanford, Calif.) was refrigerated and assayed within 1 hour (hr) after blood was drawn. One to thirty microliters (μl) of whole blood was added to the lysis solution to a final volume of 150 μl containing 50% Blood Lysis Buffer, at least 1 mg per ml proteinase K (e.g., 2 mg/ml), and H₂O. The Lysis Mixture reagent commercially available, e.g., in Panomics's QuantiGene® Explore Kit or as catalog number QG0502 or QP0522, was used as the Blood Lysis Buffer in these experiments; as noted previously, a large number of suitable buffers can be prepared by one of skill in the art (for example, the capture diluent described in Collins M L et al. (1997) Nucleic Acid Research 25:2979-2984 (127 mM LiCl, 5% lithium lauroyl sulfate, 9 mM EDTA, 50 mM HEPES (pH 7.5), 0.05% hespan (DuPont Pharmaceuticals), 0.05% ProClin 300 (Supelco), 0.2% casein (Research Organics, Hammarsten quality)). The mixture was shaken at 1000 rpm at 60° C. for 1 hour in a heated shaker (Vortemp) to lyse the cells. The lysate was then transferred to an assay well in a 96-well plate covalently coated with capture probe oligo (5′-CACTTCACTTTCTTTCCAAGAG-3′, SEQ ID NO:1). The probe set for a target gene, containing 50, 100, and 200 fmol of CE, BP, and LE, respectively, was added to the blood lysate and incubated for 16 hr at 53° C. (This incubation is optionally performed, e.g., at 58° C. instead.) The well was washed three times with 200 μl Wash Buffer (0.1×SSC, 0.3% lithium lauryl sulfate), followed by sequential hybridization at 53° C. for 1 hour with 100 μl of a 1:1000 dilution of branched-DNA amplifier (Panomics) and 46° C. for 1 hour with 100 μl of 50 fmol of 3′-alkaline phosphatase-conjugated label probe oligo (5′-AAGTACGACAACCACATC-3′, SEQ ID NO:2), with three washes after each incubation. After a final wash, the alkaline phosphatase substrate dioxetane (Panomics) was added to wells and incubated at 46° C. for 30 minutes (min) to develop the luminescent signal, which was detected using a Lmax microliter plate luminometer (Molecular Device).

Singleplex Assay for PAXgene® Stabilized Blood

PAXgene® stabilized blood was prepared according to the manufacturer's protocol (PreAnalytiX, Hombrechtikon, Switzerland). 9.5 ml stabilized blood is equivalent of 2.5 ml of whole blood. After 16 hr storage at room temperature, the stabilized blood was centrifuged for 5 min at 3000 g. The supernatant was removed by decanting or pipetting. The pellet was sequentially washed with H₂O (1000 μl per ml of stabilized blood) and 2 M LiCl (400 μl per ml of stabilized blood), before being solubilized at 60° C. with shaking for 30 minutes in Pax Lysis Buffer (265 μl per ml of stabilized blood) with 0.25 mg per ml proteinase K. In these experiments, the Homogenizing Solution commercially available from Panomics, catalog number QG0515, was used as the Pax Lysis Buffer; it will be evident that a large number of suitable buffers can be prepared by one of skill in the art (e.g., buffers including a chaotropic agent such as guanidine HCl and/or a detergent such as SDS). One to thirty μl of lysate, corresponding to the same volume of the original whole blood, was mixed with 75 μl of Blood Lysis Buffer and H₂O to a final volume of 150 μl. The mixture was transferred to an assay well in a 96-well plate coated with capture probe. The probe set for a target gene, containing 50, 100, and 200 fmol of CE, BP, and LE, respectively, was added to the lysate and incubated for 16 hr at 53° C. (This incubation is optionally performed, e.g., at 58° C. instead.) Subsequent steps were the same as the post 16 hr hybridization steps described in “Singleplex assay for whole blood” above.

Multiplex Assay

A panel of 10 oligonucleotide capture probes, each with a unique sequence of 15 bases, were synthesized with a 5′-amino linker (BioSearch, San Carlos, Calif.) and each was covalently linked to carboxylated fluorescent-encoded beads (Luminex, Austin, Tex.) following the recommended conjugation procedure (one capture probe per identifiable set of the beads). Beads conjugated with different capture probes were pooled in equal proportions before use. One hundred microliters of whole blood lysate or PAXgene® blood lysate prepared above were mixed with the multiplex panel probe sets and the pooled capture beads (2000 beads each type) in a round bottom well and hybridized for 16 hours at 53° C. in a final volume of 110 μl. (The incubation is optionally performed, e.g., at 58° C. instead.) The assay mix was transferred to a MultiScreen filter plate (Milipore), and unbound material was filter-washed from the wells three times with Wash Buffer. The plate was then hybridized at 53° C. for 1 hour with 100 μl of a 3:1000 dilution of bDNA amplifier in amplifier diluent (3M tetramethyl ammonium chloride, 0.1% Sarkosyl, 50 mM Tris-HCl, 4 mM EDTA, 4% dextran sulfate, 1% BSA and 0.5% v/v Micr-O-protect (Roche Molecular Systems, Pleasanton, Calif.)). After filter-washing twice with Wash Buffer, the plate was incubated at 46° C. for 1 hour with 100 μl of 150 fmol 5′-dT(Biotin)-conjugated label probe (Biosearch) diluted in amplifier diluent without the dextran sulfate. After two washes, streptavidin conjugated R-phycoerythrin (SA-PE, Prozyme, San Leandro, Calif.) at 6 μg/ml diluted in SAPE diluent (20 mM Tris-HCl, 400 mM Lithium Chloride, 0.1% v/v TWEEN 20, 0.1% v/v BSA, 0.5% v/v Micr-O-protect) was added and the plate was incubated at room temperature for 30 min. The beads were washed to remove unbound SA-PE, followed by analysis with Luminex® 100™ IS system (Luminex) or Bio-Plex system (Bio-Rad). The level of SA-PE fluorescence measured from each set of beads is proportional to the number of mRNA transcripts captured by that set of beads.

LPS Stimulation of Whole Blood

Fresh whole blood (Stanford Blood Center) with or without added 10 μg/ml E. coli LPS (Sigma) was incubated at 37° C. with shaking in a cell culture incubator for 30-135 minutes, before being lysed in the vessel and assayed in multiplex as described above.

Probe Design for Singleplex and Multiplex bDNA Assays

Modified probe design software (Bushnell, S. et al. (1999) “ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays” Bioinformatics 15:348-355) was developed to design probe sets for target genes in both singleplex and multiplex bDNA assays. For each target sequence, the software algorithm identifies regions that can serve as annealing templates for CEs (5-7 per gene), LEs (10-15 per gene), or BPs. Potential CEs and LEs were examined for possible interactions with other components of the multiplex assay, and CEs and LEs expected to cross-hybridize were not selected for use; CE-LE, CE-bDNA, CE-label probe, and LE-capture probe interactions having highly negative ΔG were removed to minimize non-specific hybridization. Probe sets are essentially the same for both singleplex and multiplex bDNA assays except for the portion of the CE probes that hybridize with capture probe. Three 10-plex panels were developed for assessment of the effect of common blood handling procedures. Gene names and reference sequence accession numbers are shown along with probe sets in Tables 3-5. All deoxyoligonucleotides were synthesized and HPLC purified (Biosearch, CA).

Data Analysis & Statistics

Three replicate assays (n=3) were performed for all described experimental samples unless noted otherwise. For all samples, background signal levels in the absence of target mRNAs were determined and subtracted from signals obtained in the presence of target mRNAs to get the net signal. Statistical significance of biological studies was tested using Student's t-test or ANOVA where appropriate (P<0.01).

Additional discussion of the singleplex and multiplex assays can be found in Zheng et al. (2006) “Sensitive and Quantitative Measurement of Gene Expression Directly from a Small Amount of Whole Blood” Clinical Chemistry 52:1294-1302, which is hereby incorporated by reference in its entirety.

TABLE 3 Cytokine probe set. Accession number and symbol are listed for each target, along with probe type and the sequence of the probe. SEQ ID Type Sequence NO: NM_002046 GAPDH BP CGGAGGGGCCATCCAC   3 LE cccacttgattttggagggaTTTTTaggcataggacccgtgtct   4 CE agcttcccgttctcagcctTTTTTctcttggaaagaaagt   5 LE ccttccacgataccaaagttgtTTTTTaggcataggacccgtgtct   6 CE ccttttggctcccccctTTTTTctcttggaaagaaagt   7 LE ccagtggactccacgacgtacTTTTTaggcataggacccgtgtct   8 CE tgacggtgccatggaatttTTTTTctcttggaaagaaagt   9 LE ggcatggactgtggtcatgagtTTTTTaggcataggacccgtgtct  10 LE gggtgctaagcagttggtggtTTTTTaggcataggacccgtgtct  11 LE agtcttctgggtggcagtgatTTTTTaggcataggacccgtgtct  12 BP AACATGGGGGCATCAGCA  13 BP CATGGTTCACACCCATGACG  14 BP gcaggaggcattgctgatga  15 LE cacagccttggcagcgcTTTTTaggcataggacccgtgtct  16 LE ccagtgagcttcccgttcaTTTTTaggcataggacccgtgtct  17 BP GAGGGGGCAGAGATGATGAC  18 LE tcttgaggctgttgtcatacttctTTTTTaggcataggacccgtgtct  19 CE catggatgaccttggccagTTTTTctcttggaaagaaagt  20 BP TGGAGAGCCCCGCGG  21 CE gctcagggatgaccttgccTTTTTctcttggaaagaaagt  22 LE ttctccatggtggtgaagacgTTTTTaggcataggacccgtgtct  23 LE ccatcacgccacagtttccTTTTTaggcataggacccgtgtct  24 LE gatgggatttccattgatgacaTTTTTaggcataggacccgtgtct  25 CE gcaaatgagccccagccTTTTTctcttggaaagaaagt  26 CE tctcgctcctggaagatggtTTTTTctcttggaaagaaagt  27 LE cagtagaggcagggatgatgttcTTTTTaggcataggacccgtgtct  28 BP TCAGCGCCAGCATCGC  29 NM_000584 IL8 LE aattcttgcacaaatatttgatgcTTTTTaggcataggacccgtgtct  30 LE gaaattcaaatttaaccaggaatctTTTTTaggcataggacccgtgtct  31 LE tgtattgcatctggcaaccctaTTTTTaggcataggacccgtgtct  32 BP AGTGTTGAAGTAGATTTGCTTGAAGT  33 BP AAGTTACACTTGAAAATAATTTATGTTATG  34 LE ggtaagatggtggctaatactttttTTTTTaggcataggacccgtgtct  35 BP AAAAAATCCAGGATTTCCAGCt  36 BP CTAGGGTTGCCAGATTTAACAGA  37 BP CATGTCCTCACAACATCACTGTGA  38 BP CCACTTAGAAATAAAGGAGAAACCA  39 CE tgcacccagttttccttggTTTTTctcttggaaagaaagt  40 BP GTACAATGAAAAACTATTCATTGTTTACT  41 LE ggtccagacagagctctcttccTTTTTaggcataggacccgtgtct  42 BP TTTTTTGTAGATTCAAATAAATAATACTTTA  43 BP GCTTCAAATATCACATTCTAGCAAAC  44 BP CAAAAACTTCTCCACAACCCTC  45 LE catataagtatgttctggatatttcatgTTTTTaggcataggacccgtgtct  46 LE ccattcaattcctgaaattaaagttTTTTTaggcataggacccgtgtct  47 LE ttggataccacagagaatgaatttTTTTTaggcataggacccgtgtct  48 LE ttctcccgtgcaatatctaggaTTTTTaggcataggacccgtgtct  49 BP ATAAAACATCATTTAATATCTAAAATAAAAT  50 BP CAACAGACCCACACAATACATGA  51 LE ttcactggcatcttcactgattcTTTTTaggcataggacccgtgtct  52 LE caatgattcatcttctatttttccaTTTTTaggcataggacccgtgtct  53 LE aaatttactataacatctttataactattcaatTTTTTaggcataggacccgtgtct  54 LE aggcacagtggaacaaggactTTTTTaggcataggacccgtgtct  55 CE cggatattctcttggcccttTTTTTctcttggaaagaaagt  56 CE ttttatgaattctcagccctcttTTTTTctcttggaaagaaagt  57 BP TAAAAACCCTGATTGAAATTTATCTA  58 LE ggcctcaattttgctatttgtataTTTTTaggcataggacccgtgtct  59 BP TTAAATAAATACATAAATAATAAATAGGTTAAT  60 BP ATGAAAAAACTTAAAGTGCTTCCA  61 CE tgtggatcctggctagcagaTTTTTctcttggaaagaaagt  62 LE attgtcccatcatttttatgtgatTTTTTaggcataggacccgtgtct  63 BP AAATCCTTATATTTAAAAATTATTTGTTG  64 CE acccaattgtttgtttgtttaatcTTTTTctcttggaaagaaagt  65 LE aaatttgactttatggcaaaatttTTTTTaggcataggacccgtgtct  66 NM_000600 IL6 BP CTGCAGGAACTCCTTAAAGCTG  67 LE aactggaccgaaggcgctTTTTTaggcataggacccgtgtct  68 LE aagttctgtgcccagtggacaTTTTTaggcataggacccgtgtct  69 LE tgtgcctgcagcttcgtcaTTTTTaggcataggacccgtgtct  70 LE ctgcaggaactggatcaggacTTTTTaggcataggacccgtgtct  71 BP CCTCAAACTCCAAAAGACCAGTG  72 LE gcatctagattctttgcctttttTTTTTaggcataggacccgtgtct  73 CE gagcttctctttcgttcccgTTTTTctcttggaaagaaagt  74 CE agccccagggagaaggcTTTTTctcttggaaagaaagt  75 LE gaatttgtttgtcaattcgttctgTTTTTaggcataggacccgtgtct  76 LE gatgccgtcgaggatgtaccTTTTTaggcataggacccgtgtct  77 BP TTTGGAAGGTTCAGGTTGTTTT  78 CE tgtggagaaggagttcatagctgTTTTTctcttggaaagaaagt  79 LE ggcttgttcctcactactctcaaTTTTTaggcataggacccgtgtct  80 LE atctgttctggaggtactctaggtataTTTTTaggcataggacccgtgtct  81 LE ttttgtactcatctgcacagctctTTTTTaggcataggacccgtgtct  82 LE gcaggcaacaccaggagcTTTTTaggcataggacccgtgtct  83 LE ggtttctgaccagaagaaggaatgTTTTTaggcataggacccgtgtct  84 LE tgcccatgctacatttgccTTTTTaggcataggacccgtgtct  85 LE aagaggtgagtggctgtctgtgTTTTTaggcataggacccgtgtct  86 BP TGGGGCGGCTACATCTTT  87 LE gcatccatctttttcagccatcTTTTTaggcataggacccgtgtct  88 LE atgattttcaccaggcaagtctTTTTTaggcataggacccgtgtct  89 CE tgtctcctttctcagggctgaTTTTTctcttggaaagaaagt  90 BP TGGGGCAGGGAAGGCA  91 LE gcaggctggcatttgtggTTTTTaggcataggacccgtgtct  92 LE ctgccagtgcctctttgctTTTTTaggcataggacccgtgtct  93 LE tgtcctgcagccactggttcTTTTTaggcataggacccgtgtct  94 CE gaagagccctcaggctggaTTTTTctcttggaaagaaagt  95 BP CCCATTAACAACAACAATCTGAGG  96 BP TTGGGTCAGGGGTGGTTATT  97 BP GGAATCTTCTCCTGGGGGTAC  98 LE cgcagaatgagatgagttgtcaTTTTTaggcataggacccgtgtct  99 LE ggctcctggaggcgagataTTTTTaggcataggacccgtgtct 100 CE cctcattgaatccagattggaaTTTTTctcttggaaagaaagt 101 BP GCTTTCACACATGTTACTCTTGTTACA 102 NM_000619 IFNG BP AAATGCCTAAGAAAAGAGTTCCA 103 BP TGCATTAAAATATTTCTTAAGGTTTTCT 104 BP AAAAAGTTTGAAGTAAAAGGAGACAAT 105 LE gcttcttttacatatgggtcctggTTTTTaggcataggacccgtgtct 106 LE gcaggcaggacaaccattactgTTTTTaggcataggacccgtgtct 107 BP AATAAATAGATTTAGATTTAAAATTCAAATATT 108 LE aaaaacttgacattcatgtcttccTTTTTaggcataggacccgtgtct 109 BP GGATGCTCTTCGACCTTGAAAC 110 CE tctcgtttctttttgttgctattgTTTTTctcttggaaagaaagt 111 LE aatacttatttgattgatgagtctaaaaatTTTTTaggcataggacccgtgtct 112 CE atattccccatataaataatgttaaatattTTTTTctcttggaaagaaagt 113 CE ttggctctgcattatttttctgtTTTTTctcttggaaagaaagt 114 LE tggacattcaagtcagttaccgaTTTTTaggcataggacccgtgtct 115 LE agcatctgactcctttttcgcTTTTTaggcataggacccgtgtct 116 BP GATGCTCTGGTCATCTTTAAAGTTTTT 117 LE ataattagtcagcttttcgaagtcaTTTTTaggcataggacccgtgtct 118 LE cgacagttcagccatcacttggTTTTTaggcataggacccgtgtct 119 LE ttatccgctacatctgaatgaccTTTTTaggcataggacccgtgtct 120 CE atgagttcatgtattgctttgcgtTTTTTctcttggaaagaaagt 121 LE ttgatggtctccacactcttttgTTTTTaggcataggacccgtgtct 122 CE ttccctgttttagctgctggTTTTTctcttggaaagaaagt 123 CE cactctcctctttccaattcttcaTTTTTTTctcttggaaagaaagt 124 NM_000758 CSF2 LE gcagtgtctctactcaggttcaggTTTTTaggcataggacccgtgtct 125 BP CCGCAGGCCCTGCTTG 126 BP GGGCTGGGCGAGCGG 127 LE gggttgcacaggaagtttccTTTTTaggcataggacccgtgtct 128 LE caggccacagtgcccaagTTTTTaggcataggacccgtgtct 129 BP GGGGTTGGAGGGCAGTGC 130 BP TCATGGTCAAGGGGCCCT 131 LE agcagaaagtccttcaggttctcTTTTTaggcataggacccgtgtct 132 CE tgagcttggtgaggctgccTTTTTctcttggaaagaaagt 133 CE agcagcaggctctgcagcTTTTTctcttggaaagaaagt 134 LE tgtaggcaggtcggctcctTTTTTaggcataggacccgtgtct 135 LE tttgaaactttcaaaggtgataatctTTTTTaggcataggacccgtgtct 136 LE tggatggcattcacatgctcTTTTTaggcataggacccgtgtct 137 BP CCAGGGCTGCGTGCTG 138 CE tacagctccaggcgggtcTTTTTctcttggaaagaaagt 139 LE ctcactcctggactggctccTTTTTaggcataggacccgtgtct 140 BP CAGCAGTCAAAGGGGATACA 141 LE ttctactgtttcattcatctcagcaTTTTTaggcataggacccgtgtct 142 LE ggaggtcaaacatttctgagatgacTTTTTaggcataggacccgtgtct 143 BP AGACGCCGGGCCTCC 144 CE gcgggtgcagagatgctgTTTTTctcttggaaagaaagt 145 CE tgcttgtagtggctggccaTTTTTctcttggaaagaaagt 146 NM_000572 IL10 LE gtcttcactctgctgaaggcatTTTTTaggcataggacccgtgtct 147 CE ctgggtcttggttctcagcttTTTTTctcttggaaagaaagt 148 BP GGTAAAACTGGATCATCTCAGACAA 149 LE tgatgaagatgtcaaactcactcatTTTTTaggcataggacccgtgtct 150 BP gactgggtgccctggcc 151 LE tgtcctagagtctatagagtcgccaTTTTTaggcataggacccgtgtct 152 BP GGCTTTGTAGATGCCTTTCTCT 153 LE TaggcaggttgcctgggaTTTTTaggcataggacccgtgtct 154 LE cattgtcatgtaggcttctatgtagtTTTTTaggcataggacccgtgtct 155 CE ctcggagatctcgaagcatgtTTTTTctcttggaaagaaagt 156 BP GGGGCATCACCTCCTCCA 157 CE ccgattttggagacctctaatttaTTTTTctcttggaaagaaagt 158 CE gctgatccttcatttgaaagaaaTTTTTctcttggaaagaaagt 159 LE tggagcttattaaaggcattcttTTTTTaggcataggacccgtgtct 160 CE agtgggtgcagctgttctcaTTTTTctcttggaaagaaagt 161 LE gctatcccagagccccagatTTTTTaggcataggacccgtgtct 162 LE ccctgatgtctcagtttcgtatcttTTTTTaggcataggacccgtgtct 163 LE actcctttaacaacaagttgtccaTTTTTaggcataggacccgtgtct 164 LE cacctgctccacggccttTTTTTaggcataggacccgtgtct 165 BP GTTCACATGCGCCTTGATGT 166 LE aatcgatgacagcgccgtaTTTTTaggcataggacccgtgtct 167 BP GCTCTTGTTTTCACAGGGAAGA 168 LE ggcttggcaacccaggtaacTTTTTaggcataggacccgtgtct 169 LE caggttctcccccagggaTTTTTaggcataggacccgtgtct 170 CE gcctcagcctgagggtcttTTTTTctcttggaaagaaagt 171 LE ccttaaagtcctccagcaaggTTTTTaggcataggacccgtgtct 172 NM_000594 TNF LE gcggctgatggtgtgggTTTTTaggcataggacccgtgtct 173 LE aggtacaggccctctgatggTTTTTaggcataggacccgtgtct 174 LE tcactccaaagtgcagcaggTTTTTaggcataggacccgtgtct 175 CE tcgggccgattgatctcaTTTTTctcttggaaagaaagt 176 BP AGGCTTGTCACTCGGGGTT 177 BP GAGGTCCCTGGGGAACTCTT 178 LE gcgctgagtcggtcaccctTTTTTaggcataggacccgtgtct 179 LE tctccagctggaagaccccTTTTTaggcataggacccgtgtct 180 LE agactcggcaaagtcgagatagTTTTTaggcataggacccgtgtct 181 CE gtctggtaggagacggcgatTTTTTctcttggaaagaaagt 182 BP TGGGGCAGGGGAGGC 183 BP CCCCTCTGGGGTCTCCCTC 184 LE caggagggcattggcccTTTTTaggcataggacccgtgtct 185 BP ggccagagggctgattagaga 186 LE gtcctcctcacagggcaatgTTTTTaggcataggacccgtgtct 187 CE tcccagatagatgggctcatacTTTTTctcttggaaagaaagt 188 LE cagggcttggcctcagcTTTTTaggcataggacccgtgtct 189 BP tgaagaggacctgggagtagatg 190 BP GGGCAGCCTTGGCCCT 191 CE cgagaagatgatctgactgcctgTTTTTctcttggaaagaaagt 192 LE cagaagaggttgagggtgtctgaTTTTTaggcataggacccgtgtct 193 LE gctgcccctcagcttgagTTTTTctcttggaaagaaagt 194 LE ggcggttcagccactggaTTTTTaggcataggacccgtgtct 195 LE caccaccagctggttatctctcTTTTTaggcataggacccgtgtct 196 LE ggtttgctacaacatgggctacTTTTTaggcataggacccgtgtct 197 BP AGGAGGGGGTAATAAAGGGAT 198 CE cccccaattctctttttgagcTTTTTctcttggaaagaaagt 199 BP TGGCAGGGGCTCTTGATG 200 BP CCCTCTGGGGGCCGA 201 LE gcttgggttccgaccctaagTTTTTaggcataggacccgtgtct 202 LE atcccaaagtagacctgcccTTTTTaggcataggacccgtgtct 203 BP GTTTGGGAAGGTTGGATGTTC 204 LE gcagagaggaggttgaccttgTTTTTaggcataggacccgtgtct 205 LE tgaggagcacatgggtggagTTTTTaggcataggacccgtgtct 206 LE agctccacgccattggcTTTTTaggcataggacccgtgtct 207 NM_000586 IL2 LE aaacttaaatgtgagcatcctggTTTTTaggcataggacccgtgtct 208 CE ctccagaggtttgagttcttcttcTTTTTctcttggaaagaaagt 209 LE agtgggaagcacttaattatcaagTTTTTaggcataggacccgtgtct 210 BP CCTGGGTCTTAAGTGAAAGTTTTT 211 LE gctgtgttttctttgtagaacttgaTTTTTaggcataggacccgtgtct 212 LE gctttgagctaaatttagcacttcTTTTTaggcataggacccgtgtct 213 BP AGCATATTCACACATGAATGTTGTT 214 LE attacgttgatattgctgattaagccTTTTTaggcataggacccgtgtct 215 LE agtaggtgcactgtttgtgacaagTTTTTaggcataggacccgtgtct 216 CE tcagatccctttagttccagaactTTTTTctcttggaaagaaagt 217 CE aataaatagaaggcctgatatgttttaTTTTTctcttggaaagaaagt 218 LE tcagtgttgagatgatgctttgacTTTTTaggcataggacccgtgtct 219 BP AAAAGGTAATCCATCTGTTCAGAAA 220 LE ttccacaatggttgctgtctcatcTTTTTaggcataggacccgtgtct 221 LE cagcagtaaatgctccagttgtaTTTTTaggcataggacccgtgtct 222 LE tagacactgaagatgtttcagttctgTTTTTaggcataggacccgtgtct 223 CE tggccttcttgggcatgtaTTTTTctcttggaaagaaagt 224 LE aatagttacaataggtagcaaaccatacTTTTTaggcataggacccgtgtct 225 BP ATTCAACAATAAATATAAAATTTAAATATTTA 226 BP TTCCATTCAAAATCATCTGTAAATC 227 CE tgagtttgggattcttgtaattaataaTTTTTctcttggaaagaaagt 228 NM_000576 IL1B CE ggagagctttcagttcatatggaTTTTTctcttggaaagaaagt 229 LE ttatcccatgtgtcgaagaagataTTTTTaggcataggacccgtgtct 230 BP ccagacatcaccaagctttttt 231 CE tgaagcccttgctgtagtggtTTTTTctctcggaaagaaagt 232 LE catcgtgcacataagcctcgTTTTTaggcataggacccgtgtct 233 CE cctggaaggtctgtgggcaTTTTTctcttggaaagaaagt 234 LE gcagttcagtgatcgtacaggtgTTTTTaggcataggacccgtgtct 235 LE ggtcggagattcgtagctggTTTTTaggcataggacccgtgtct 236 CE gcagaggtccaggtcctggTTTTTctcttggaaagaaagt 237 LE gggaaccagcatcttcctcaTTTTTaggcataggacccgtgtct 238 CE ccatatcctgtccctggaggtTTTTTctcttggaaagaaagt 239 LE atggagaacaccacttgttgctTTTTTaggcataggacccgtgtct 240 LE atgccgccatccagaggTTTTTaggcataggacccgtgtct 241 LE aggccacaggtattttgtcattTTTTTaggcataggacccgtgtct 242 CE aaagaaggtgctcaggtcattctTTTTTctcttggaaagaaagt 243 LE actttcttctccttgtacaaaggacTTTTTaggcataggacccgtgtct 244 BP ACTGACGCGGCCTGCC 245 LE gccatcagcttcaaagaacaagTTTTTaggcataggacccgtgtct 246 LE gctgtgagtcccggagcgtTTTTTaggcataggacccgtgtct 247 CE attcttttccttgaggcccaTTTTTctcttggaaagaaagt 248 LE gcttgtccatggccacaacaTTTTTaggcataggacccgtgtct 249 LE aaggagcacttcacctgtttaggTTTTTaggcataggacccgtgtct 250 LE ggttcttcttcaaagatgaagggTTTTTaggcataggacccgtgtct 251 NM_003376 VEGF CE atctttctttggtctgcattcacTTTTTctcttggaaagaaagt 252 CE aaggctccaatgcacccaTTTTTctcttggaaagaaagt 253 LE ggcccacagggaacgctTTTTTaggcataggacccgtgtct 254 BP GCAGCCCCCGCATCG 255 LE gatgattctgccctcctccttTTTTTaggcataggacccgtgtct 256 LE accagggtctcgattggatgTTTTTaggcataggacccgtgtct 257 LE tgggaccacttggcatggTITTTaggcataggacccgtgtct 258 LE tccatgaacttcaccacttcgtTTTTTaggcataggacccgtgtct 259 LE ttgcgctttcgtttttgcTTTTTaggcataggacccgtgtct 260 LE tggaggtagagcagcaaggcTTTTTaggcataggacccgtgtct 261 LE gcttgaagatgtactcgatctcatcTTTTTaggcataggacccgtgtct 262 LE ctgattttttttcttgtcttgctctTTTTTaggcataggacccgtgtct 263 LE agggtactcctggaagatgtccTTTTTaggcataggacccgtgtct 264 BP CTCCTCAGTGGGCACACACTC 265 LE caggccctcgtcattgcaTTTTTaggcataggacccgtgtct 266 CE ccctttccctttcctcgaaTTTTTctcttggaaagaaagt 267 CE ccaggacttataccgggatttcTTTTTctcttggaaagaaagt 268 LE gcagtagctgcgctgatagacaTTTTTaggcataggacccgtgtct 269 BP CATCAGGGGCACACAGGATG 270 LE atttgttgtgctgtaggaagctcTTTTTaggcataggacccgtgtct 271 CE ctgccatgggtgcagccTTTTTctcttggaaagaaagt 272 CE atctctcctatgtgctggcctTTTTTctcttggaaagaaagt 273 LE TaatctgcatggtgatgttggaTTTTTaggcataggacccgtgtct 274 CE tggtgaggtttgatccgcaTTTTTctcttggaaagaaagt 275

TABLE 4 Apoptosis 1 probe set. Accession number and symbol are listed for each target, along with probe type and the sequence of the probe. SEQ ID Type Sequence NO: NM_001188 BAK1 LE ccatgctggtagacgtgtagggTTTTTaggcataggacccgtgtct 276 LE tctctgccgtgggctgcTTTTTaggcataggacccgtgtct 277 LE gccccaattgatgccactcTTTTTaggcataggacccgtgtct 278 BP GGGGCAGCCACCCCTTC 279 BP gggaggacctgggccttg 280 BP GGCGGTAAAAAACGTAGCTG 281 BP CGGAAAACCTCCTCTGTGTCC 282 BP TGGCGAGCTGCCGTCC 283 LE ccaagttcagggctgccacTTTTTaggcataggacccgtgtct 284 CE cagcctgccgggatcctTTTTTctcttggaaagaaagt 285 BP ggcctaggaagccagtcagg 286 LE ccagaagagccaccacacgTTTTTaggcataggacccgtgtct 287 LE gaccatctctgggtcggcaTTTTTaggcataggacccgtgtct 288 LE aggtgctgcaacatggtctgTTTTTaggcataggacccgtgtct 289 BP AGCAGAGGGCAGGGCAG 290 BP TCTTGGTGAAGTACTCATAGGCAT 291 BP ccagccacccctctgtgc 292 CE ccccgaagccatttttcaTTTTTctcttggaaagaaagt 293 CE tgctaggttgcagaggtaaggtTTTTTctcttggaaagaaagt 294 LE tcaaacaggctggtggcaaTTTTTaggcataggacccgtgtct 295 LE cacctgccccatggtgcTTTTTaggcataggacccgtgtct 296 LE gttcaggatgggaccattgcTTTTTaggcataggacccgtgtct 297 LE aatccaccgggcaatgcTTTTTaggcataggacccgtgtct 298 LE ttgatgtcgtccccgatgaTTTTTaggcataggacccgtgtct 299 CE tgggctacctgctcctcagaTTTTTctcttggaaagaaagt 300 BP gaactctgagtcacagcgtcgg 301 LE ccacgaagcgggtcacctTTTTTaggcataggacccgtgtct 302 LE ggtctcagtggaggacgggatTTTTTaggcataggacccgtgtct 303 BP AGTGATGCAGCATGAAGTCGA 304 CE ccagacggtagccgaagcTTTTTctcttggaaagaaagt 305 CE agcctcctgttcctgctgatTTTTTctcttggaaagaaagt 306 LE gctctccgcactcctgcctTTTTTaggcataggacccgtgtct 307 NM_000565 IL6R LE gcacgaagctgcaccacgtTTTTTaggcataggacccgtgtct 308 CE ttcagcccgatatctgagctcTTTTTctcttggaaagaaagt 309 LE aaaccgtagtctgtagaaagatgagtTTTTTaggcataggacccgtgtct 310 LE ccaggtgacactgagccagcTTTTTaggcataggacccgtgtct 311 LE cgacactaccggcgacgcaTTTTTaggcataggacccgtgtct 312 LE gcagtgactgtgatgttggcaTTTTTaggcataggacccgtgtct 313 BP CATGGACACTATGTAGAAAGAGCTG 314 BP gctggaggtccttgaccatc 315 CE tgagttttgctgaacttgctccTTTTTctcttggaaagaaagt 316 LE ttctgtccaaggcgtgccTTTTTaggcataggacccgtgtct 317 BP CATGGCCTCCGGGCTC 318 LE catgttgcgaatgtctttgaccgTTTTTaggcataggacccgtgtct 319 BP GGGGGTTTCTGGCCACG 320 LE caccaagagcacagcctttgtTTTTTaggcataggacccgtgtct 321 LE gcgtcgtggatgacacagtgatTTTTTaggcataggacccgtgtct 322 CE ccggactgttctgaaacttcctTTTTTctcctggaaagaaagt 323 LE gattccacaaccctgaaaggttTTTTTaggcataggacccgtgtct 324 LE gactcctgggaatactggcacTTTTTaggcataggacccgtgtct 325 CE gcctcaggccgctccagTTTTTctcttggaaagaaagt 326 CE tctccctccgggactgctTTTTTctcctggaaagaaagt 327 LE ggcggatcaggctgcaaTTTTTaggcataggacccgtgtct 328 BP AACTGGCAGGAGAACTTCTGG 329 BP TCCAGGAGTGGGGGTCTTG 330 LE ggctcctggaagtcttcggTTTTTaggcataggacccgtgtct 331 BP cactcgctccactcgcct 332 CE tgcccgaactcctcctggTTTTTctcttggaaagaaagt 333 NM_138578 BCL2L1 LE cggttgaagcgttcctggTTTTTaggcataggacccgtgtct 334 LE gctgcatcgttcccatagagttcTTTTTaggcataggacccgtgtct 335 LE gccatccaagctgcgatcTTTTTaggcataggacccgtgtct 336 CE gctcccggttgctctgagaTTTTTctcttggaaagaaagt 337 BP CACAAAAGTATCCCAGCCGC 338 BP CACAGTGCCCCGCCG 339 LE cgactcaccaatacctgcatctTTTTTaggcataggacccgtgtct 340 LE gggcctcagtcctgttctcttTTTTTaggcataggacccgtgtct 341 BP CACCTCCCGGGCATCC 342 LE gctgggatgtcaggtcactgaaTTTTTaggcataggacccgtgtct 343 BP TGGCACTGGGGGTCTCCA 344 BP TGCCCGCCGGTACCG 345 LE cgttctcctggatccaaggcTTTTTaggcataggacccgtgtct 346 CE tgtatcctttctgggaaagcttTTTTTctcttggaaagaaagt 347 CE cctccctcagcgcttgctTTTTTctcttggaaagaaagt 348 LE cctgttcaaagctctgatatgctgTTTTTaggcataggacccgtgtct 349 LE caggatgggttgccattgaTTTTTaggcataggacccgtgtct 350 LE tctccgattcagtcccttctgTTTTTaggcataggacccgtgtct 351 BP TTACTGCTGCCATGGGGAT 352 LE ccttgtctacgctttccacgTTTTTaggcataggacccgtgtct 353 LE gtaggagagaaagtcaaccaccaTTTTTaggcataggacccgtgtct 354 LE cagttcaaactcgtcgcctgTTTTTaggcataggacccgtgtct 355 CE aaactgctgctgtggccagTTTTTctcttggaaagaaagt 356 LE cgaccccagtttaccccaTTTTTaggcataggacccgtgtct 357 BP ccacatcactaaactgactccagc 358 LE tggctccattcaccgcgTTTTTaggcataggacccgtgtct 359 LE tctaggtggtcattcaggtaagtgTTTTTaggcataggacccgtgtct 360 BP AAGGAGAAAAAGGCCACAATG 361 CE gggctgtctgccaggtgcTTTTTctcttggaaagaaagt 362 LE tcccggaagagttcattcactaTTTTTaggcataggacccgtgtct 363 CE ccctttcggctctcggctTTTTTctcttggaaagaaagt 364 BP TCCCTGGGGTGATGTGGA 365 NM_003879 CFLAR LE tctgctgttccaatcatacatgtaTTTTTaggcataggacccgtgtct 366 CE gccctcgcttctgagcctTTTTTctcttggaaagaaagt 367 LE tgaattccacattcttcatcgcTTTTTaggcataggacccgtgtct 368 LE tggcctcccaaagtgctgTTTTTaggcataggacccgtgtct 369 CE gcccagccttttggtttcttaTTTTTctcttggaaagaaagt 370 LE ttcttgtctcagtttctgggagaTTTTTaggcataggacccgtgtct 371 LE tggcccatccacctccaTTTTTaggcataggacccgtgtct 372 BP TGGCCCTCTGACACCACATAG 373 LE gcgtttaccatgttggccaTTTTTaggcataggacccgtgtct 374 LE cataatatttctccttggcagaaacTTTTTaggcataggacccgtgtct 375 LE ggtgagctgtgagactgctccaTTTTTaggcataggacccgtgtct 376 LE ttccctgctagataagggcatTTTTTaggcataggacccgtgtct 377 LE ggattacaggtgtgagccactacTTTTTaggcataggacccgtgtct 378 BP TTCTGAATAAAAAACATCTTTGGC 379 LE ggcactgcaggtacagggacTTTTTaggcataggacccgtgtct 380 BP CACAGGCTCCAGAAGAAGTCAG 381 LE tgtgtaggagaggataagtttctttctTTTTTaggcataggacccgtgtct 382 CE cagagtgtgctgcagccagaTTTTTctcttggaaagaaagt 383 CE agaggctgctgttctccagcTTTTTctcttggaaagaaagt 384 LE gccattgagttcaatgtgaagatTTTTTaggcataggacccgtgtct 385 CE ggctggtctcgaactcctgaTTTTTctcttggaaagaaagt 386 LE cttctcggtgaactgtgcacaTTTTTaggcataggacccgtgtct 387 LE atttttgcatttttactagggacaTTTTTaggcataggacccgtgtct 388 CE ccaggagtgggcgttttctTTTTTctcttggaaagaaagt 389 BP CCTGAAGTGATCTGCCCTCCT 390 LE gcagggacatgtccgcagtaTTTTTaggcataggacccgtgtct 391 NM_000639 TNFSF6 BP TCCTGGGGATACTTAGAGTTCCT 392 BP CCCGGAAGTATACTTTGGAATATA 393 CE ttggacttgcctgttaaatggTTTTTctcttggaaagaaagt 394 LE agagctgaaacatccccaggTTTTTaggcataggacccgtgtct 395 LE tcccctccatcatcaccagaTTTTTaggcataggacccgtgtct 396 LE catgtagaccttgtggctcaggTTTTTaggcataggacccgtgtct 397 LE atcacaaggccacccttcttaTTTTTaggcataggacccgtgtct 398 BP GCGGGCCCACATCTGC 399 CE ccagctccttctgtaggtggaTTTTTctcttggaaagaaagt 400 LE ggcaggttgttgcaagattgacTTTTTaggcataggacccgtgtct 401 LE cccaatcctaccaaggcaacTTTTTaggcataggacccgtgtct 402 BP ccagaggcatggaccttgag 403 CE ggtggcagcggtagtggagTTTTTctcttggaaagaaagt 404 CE tggttccctctcttcttcaggTTTTTctcttggaaagaaagt 405 LE ccagtagtgcagtagctcatcatctTTTTTaggcataggacccgtgtct 406 CE gctggtagactctcggagttctgTTTTTctcttggaaagaaagt 407 LE aagatgatgctgtgtgcatctgTTTTTaggcataggacccgtgtct 408 LE ggagacacaggcctgtgctgTTTTTaggcataggacccgtgtct 409 CE tgcccccaggtagctgctTTTTTctcttggaaagaaagt 410 BP CAGAACCATGAAAAACATCACAA 411 BP AATTCCATAGGTGTCTTCCCATT 412 BP tacttcactccagaaagcaggac 413 CE gcggcggaggtggtagtTTTTTctcttggaaagaaagt 414 BP TTTTCAGGGGGTGGACTGG 415 BP gccactttcctcagctccttt 416 LE caaagtacagcccagtttcattgTTTTTaggcataggacccgtgtct 417 BP GCAGTGGTGGCGGCG 418 LE ggtggcctatttgcttctccaTTTTTaggcataggacccgtgtct 419 NM_001101 ACTB LE cgtggtggtgaagctgtagcTTTTTaggcataggacccgtgtct 420 BP CGCAGGATGGCATGGGG 421 LE acaggtctttgcggatgtccTTTTTaggcataggacccgtgtct 422 CE acaggactccatgcccaggTTTTTctcttggaaagaaagt 423 BP CGATTTCCCGCTCGGC 424 LE gggcacagtgtgggtgaccTTTTTaggcataggacccgtgtct 425 LE agacagcactgtgttggcgtTTTTTaggcataggacccgtgtct 426 LE tcggtcagcagcacgggTTTTTaggcataggacccgtgtct 427 LE ccagggcgacgtagcacaTTTTTaggcataggacccgtgtct 428 LE catgaggtagtcagtcaggtcccTTTTTaggcataggacccgtgtct 429 CE ctcgtagctcttctccagggaTTTTTctcttggaaagaaagt 430 LE tctcaaacatgatctgggtcatcTTTTTaggcataggacccgtgtct 431 BP TGGCTGGGGTGTTGAAGG 432 CE ggagctggaagcagccgtTTTTTctcttggaaagaaagt 433 LE ggccatctcttgctcgaagtTTTTTaggcataggacccgtgtct 434 CE aaggaaggctggaagagtgcTTTTTctcttggaaagaaagt 435 CE cgcgctcggtgaggatcttTTTTTctcttggaaagaaagt 436 LE ctcagggcagcggaaccTTTTTaggcataggacccgtgtct 437 LE ccgtcaccggagtccatcaTTTTTaggcataggacccgtgtct 438 LE gagggcatacccctcgtagatTTTTTaggcataggacccgtgtct 439 BP ACGTCACACTTCATGATGGAGTT 440 LE gcttctccttaatgtcacgcaTTTTTaggcataggacccgtgtct 441 BP acctggccgtcaggcag 442 LE cgatgccagtggtacggcTTTTTaggcataggacccgtgtct 443 LE cagcctggatagcaacgtacaTTTTTaggcataggacccgtgtct 444 LE gaaggtagtttcgtggatgccTTTTTaggcataggacccgtgtct 445 CE gctcattgccaatggtgatgTTTTTctcttggaaagaaagt 446 LE cagaggcgtacagggatagcaTTTTTaggcataggacccgtgtct 447 BP GGCCAGCCAGGTCCAGA 448 CE ttctcgcggttggccttTTTTTctcttggaaagaaagt 449 BP GGGGTTCAGGGGGGCC 450 NM_000043 TNFRSF6 LE gaactgaatttgttgtttttcactctTTTTTaggcataggacccgtgtct 451 LE ttgccactgtttcaggatttaaTTTTTaggcataggacccgtgtct 452 LE tccatgaagttgatgccaattaTTTTTaggcataggacccgtgtct 453 CE gattggcttttttgagatctttaatTTTTTctcttggaaagaaagt 454 LE ccccaagttagatctggatcctTTTTTaggcataggacccgtgtct 455 LE agaccaagctttggatttcattTTTTTaggcataggacccgtgtct 456 CE cgaagcagttgaactttctgttcTTTTTctcttggaaagaaagt 457 CE tgactccagcaatagtggtgatatatTTTTTctcttggaaagaaagt 458 LE tcctctttgcacttggtgttgTTTTTaggcataggacccgtgtct 459 LE catgttttctgtacttcctttctcttTTTTTaggcataggacccgtgtct 460 LE tgctgtgtcttggacattgtcatTTTTTaggcataggacccgtgtct 461 LE tctgaagtttgaattttctgagtcaTTTTTaggcataggacccgtgtct 462 CE ggttttcctttctgtgctttctgTTTTTctcttggaaagaaagt 463 LE ctagtaatgtccttgaggatgatagtcTTTTTaggcataggacccgtgtct 464 LE agtatttacagccagctattaagaatcTTTTTaggcataggacccgtgtct 465 LE ttttcaaacactaattgcatatactcaTTTTTaggcataggacccgtgtct 466 BP GCAAAAGAAGAAGACAAAGCCA 467 LE ggttggagattcatgagaaccttTTTTTaggcataggacccgtgtct 468 BP ATGTACCCAGTAAAAAACCAAGC 469 LE cattgacaccattctttcgaacaTTTTTaggcataggacccgtgtct 470 LE ttactcaagtcaacatcagataaatttaTTTTTaggcataggacccgtgtct 471 LE caatgtgtcatacgcttctttcttTTTTTaggcataggacccgtgtct 472 LE cacccaaacaattagtggaattgTTTTTaggcataggacccgtgtct 473 LE aagcctttaacttgacttagtgtcaTTTTTaggcataggacccgtgtct 474 LE tcttgatctcatctattttggcttTTTTTaggcataggacccgtgtct 475 CE ctcttcagcgctaataaatgataaaTTTTTctcttggaaagaaagt 476 LE tgaattttctctgcaagagtacaaaTTTTTaggcataggacccgtgtct 477 NM_004103 PTK2B LE aagtactgcctggccctccTTTTTaggcataggacccgtgtct 478 LE gggccttcgcagggtttcTTTTTaggcataggacccgtgtct 479 BP GGACAAGGCCTGGGGGG 480 BP TCCAGCGGGAGGCACC 481 LE caccttcaatgcccagctgTTTTTaggcataggacccgtgtct 482 CE gctggcggatccctttaggTTTTTctcttggaaagaaagt 483 LE cttggtgctcaccctgcagTTTTTaggcataggacccgtgtct 484 CE ctgctagggatgaggttttgatTTTTTctcttggaaagaaagt 485 LE ggaactgtttgggctttaagttTTTTTaggcataggacccgtgtct 486 LE aaggtctgctggatcatcttccTTTTTaggcataggacccgtgtct 487 LE gttccgcttctcaccatctttTTTTTaggcataggacccgtgtct 488 LE ccggcagtagccgtctatgaTTTTTaggcataggacccgtgtct 489 LE gacgcactcctcctccctgTTTTTaggcataggacccgtgtct 490 LE gccaatgaccaggtccacagtTTTTTaggcataggacccgtgtct 491 LE agcgaggcgtactgctggTTTTTaggcataggacccgtgtct 492 CE acagcggtaggtctcctggtTTTTTctcttggaaagaaagt 493 LE ctgagaggtgggaccgccTTTTTaggcataggacccgtgtct 494 CE gggcctccaggtttagcatgTTTTTctcttggaaagaaagt 495 BP ACTCGGCCAGGCAGGTG 496 LE cgatgttggcgaagccgTTTTTaggcataggacccgtgtct 497 BP AATGTTCCATCCTTGAATGAGTTC 498 CE gtctgactctatgctgcagctctTTTTTctcttggaaagaaagt 499 LE cctaggatggatgatgagagagcTTTTTaggcataggacccgtgtct 500 LE ggtcagccatgttctcagcctTTTTTaggcataggacccgtgtct 501 BP GGGATCTGGGGCAGGCT 502 CE gcgagagtgttgaagaacttcatTTTTTctcttggaaagaaagt 503 LE ggctttgcgtcctgactagtcaTTTTTaggcataggacccgtgtct 504 LE tgatggacctgatctgcttgaTTTTTaggcataggacccgtgtct 505 LE gtcgggaatctctgcgtagatTTTTTaggcataggacccgtgtct 506 NM_004322 BAD BP tgctgctggttggctgct 507 LE cctgctcactcggctcaaactTTTTTaggcataggacccgtgtct 508 LE ctgggatctggaacatgctctTTTTTaggcataggacccgtgtct 509 BP tggaaggcagaggcaggta 510 LE cccccatcccttcgtcgTTTTTaggcataggacccgtgtct 511 BP CCGGAGCCTGAGGGCC 512 LE cgtagtcaaggcacagctggTTTTTaggcataggacccgtgtct 513 BP cgggtctggcctggcag 514 CE ggagctgaggctgtcggcTTTTTctcttggaaagaaagt 515 BP cccacaggaggcctggg 516 CE gagctcgcggccatagcTTTTTctcttggaaagaaagt 517 BP GCCCGCCAGGCCTCC 518 BP ACCGTAGCGCCCCCAG 519 CE agcgcctccatgatggcTTTTTctcttggaaagaaagt 520 CE gcctggcgatgatgcttgTTTTTctcttggaaagaaagt 521 BP TCCTCCGTCCCCGCG 522 LE tgggccctcatctgtctgcTTTTTaggcataggacccgtgtct 523 CE cccctggcttcctctcccTTTTTctcttggaaagaaagt 524 LE gctgtgctgcccagaggttTTTTTaggcataggacccgtgtct 525 BP GCGAGCGGCCCCG 526 CE cctgctggtgactggcgtTTTTTctcttggaaagaaagt 527 LE tcaggacctcagtctcccctcTTTTTaggcataggacccgtgtct 528 BP TGGGGCCCAGGCCC 529 LE agtcccttcttaaaggagtccacTTTTTaggcataggacccgtgtct 530 BP GGCCAACGGTGGCCC 531 CE ctctctgcagagctggagtcttTTTTTctcttggaaagaaagt 532 BP AAAGGGGCTGGGCTCCT 533 BP CGTCCCCTGCGGGGC 534 BP GGGGGGCGCCGAGC 535 LE ccggatctccacagccccTTTTTaggcataggacccgtgtct 536 LE gggtaggagctgtggcgactTTTTTaggcataggacccgtgtct 537 LE aaactcgtcactcatcctccgTTTTTaggcataggacccgtgtct 538 LE gggctgtgaggacaagatgttaTTTTTaggcataggacccgtgtct 539 NM_000633 BCL2 BP TCTTCAATACAAAATAGGGATGGTT 540 LE cggagacgacccgatggcTTTTTaggcataggacccgtgtct 541 CE tttgtgcagcgagggactgTTTTTctcttggaaagaaagt 542 BP AATCTTGATTATTATAACTCCTCTCGAT 543 BP CCCCAATTTGGAAAGTGCATAt 544 LE ctgggccagagctacatctttaTTTTTaggcataggacccgtgtct 545 LE catagaccctgtcagctgtcattcTTTTTaggcataggacccgtgtct 546 CE tctgcccctgccaaatcttTTTTTctcttggaaagaaagt 547 LE ctctgttgcccaactgcaaaTTTTTaggcataggacccgtgtct 548 CE ctcagatgttcttctccttttggTTTTTctcttggaaagaaagt 549 BP CATCTGAACACAGAGAGGTAAGTGAGc 550 BP GATGATAAGCATTTACTAATAAAACAAA 551 LE cagtgtaaagaggagtacatacagaggTTTTTaggcataggacccgtgtct 552 LE tgtggagagaatgttggcgtTTTTTaggcataggacccgtgtct 553 LE gatcacatataaatggaaggccaTTTTTaggcataggacccgtgtct 554 CE cttgtttgaactaaattgaggtgcTTTTTctcttggaaagaaagt 555 BP ACTCTATTTAACTCTGACCCTGGC 556 LE ggagggccgaggaggttTTTTTaggcataggacccgtgtct 557 CE actgttttttcattcataaagagcaTTTTTctcttggaaagaaagt 558 LE gttaagatgcagatgtgaatcccTTTTTaggcataggacccgtgtct 559 LE ggattgccctgattatttacatttTTTTTaggcataggacccgtgtct 560 CE aaatcttaagcctgccagagtttTTTTTctcttggaaagaaagt 561 LE tggcctctcttgcggagtaTTTTTaggcataggacccgtgtct 562 LE tataatcacttcctaatttttcccaTTTTTaggcataggacccgtgtct 563 LE ttccttgattctgtgactttattccTTTTTaggcataggacccgtgtct 564 CE ggctttttttagagcccttgtTTTTTctcttggaaagaaagt 565

TABLE 5 Apoptosis 2 probe set. Accession number and symbol are listed for each target, along with probe type and the sequence of the probe. SEQ ID Type Sequence NO: NM_006509 RELB CE ggctttttcttccgccgTTTTTcccttggaaagaaagt 566 LE tccacgccgtagctgtcatTTTTTaggcataggacccgtgtct 567 BP CGGCGTCTTGAACACAATGG 568 LE tgaccgtcacgggctcgacTTTTTaggcataggacccgtgtct 569 LE ccccgtttccgctccttgTTTTTaggcataggacccgtgtct 570 LE tgaaaggcaatggctcgcTTTTTaggcataggacccgtgtct 571 LE gcccgaccttcccaggagTTTTTaggcataggacccgtgtct 572 CE caatctggcggtgcacgTTTTTctcttggaaagaaagt 573 CE gccgctgcaggaagacgtTTTTTctcttggaaagaaagt 574 LE gcaaatccgcagctctgatgTTTTTaggcataggacccgtgtct 575 LE gccctgctgaacaccactgaTTTTTaggcataggacccgtgtct 576 LE tgcagaccccatcggtgaTTTTTaggcataggacccgtgtct 577 BP gggctcggaaagcacagg 578 CE aatctccaggtcctcgtagggTTTTTctcttggaaagaaagt 579 LE cgcagagcaagtagagctcctcTTTTTaggcataggacccgtgtct 580 LE atccacccggcgcatctTTTTTaggcataggacccgtgtct 581 BP ggtcgcgaggcaggtacg 582 BP ccaaggacgtcgggcatc 583 CE ccgctttccttgttaattcgTTTTTctcttggaaagaaagt 584 BP TGTTTGTGGATTTCTTGTCATAGAC 585 LE atgaggcctggaagcagatcTTTTTaggcataggacccgtgtct 586 BP GCCACCGGTGCACGGC 587 CE gtccctgctggtcccgatTTTTTctcttggaaagaaagt 588 LE tttgctctcgatgccatggTTTTTaggcataggacccgtgtct 589 BP TATGTCCTCTTTCTGCACCTTGT 590 LE tcggcctgggagaagtcaTTTTTaggcataggacccgtgtct 591 LE gggtcagagctgttcagctccTTTTTaggcataggacccgtgtct 592 NM_000389 CDKN1A BP GGGGAGGGACAGCAGCAG 593 BP AGGGGAATTGCAGAGCCC 594 LE ttttgatgatgcccccactcTTTTTaggcataggacccgtgtct 595 BP TGTCCCTTCCCCTTCCAGT 596 CE aagaattcaggtctgagtgtccagTTTTTctcctggaaagaaagt 597 CE ttgagctgcctgaggtagaactTTTTTctcttggaaagaaagt 598 BP gggtgggacaggcacctc 599 BP CCATTGAGCTGGGGGTGG 600 BP AGGGTGCCCTTCTTCTTGTG 601 BP GGAGGGATGGGGTGGATG 602 LE tgccaccacatgggacccTTTTTaggcataggacccgtgtct 603 BP GGGGGCGGTCGCTGC 604 BP CCCAGTGCAGGTCAGAGGG 605 CE tgtctgactccttgttccgctTTTTTctcttggaaagaaagt 606 CE agctggagaagaagggtaagctTTTTTctcttggaaagaaagt 607 LE caagagccaggagggtaccaTTTTTaggcataggacccgtgtct 608 CE ctcctagaaagatctactcccccTTTTTctcttggaaagaaagt 609 BP GAGGTGAGGGGACTCCAAAGT 610 LE agagccacctggagcatgagTTTTTaggcataggacccgtgtct 611 LE gctcaacactgagacgggctcTTTTTaggcataggacccgtgtct 612 BP GCTAATCAAAGTGCAATGAACTGG 613 BP GGGAGCCAAAGAGGGAAAAG 614 BP AGGGTACTGAAGGGAAAGACAAG 615 BP CCCACTCAAGGGGGCCTG 616 BP ATCATATACCCCTAACACAGAGATAAC 617 LE ccatctgtttacttctcaaatgaaaTTTTTaggcataggacccgtgtct 618 LE gggtggtctgctccagtaccTTTTTaggcataggacccgtgtct 619 LE tcacccccacagctagaggaTTTTTaggcataggacccgtgtct 620 LE caccctgcccaaccttagagTTTTTaggcataggacccgtgtct 621 BP GCCATGAGGGCAGGCG 622 CE ggtccccagctcagccctaTTTTTctcttggaaagaaagt 623 LE ccaccttccccctgcctTTTTTaggcataggacccgtgtct 624 LE aggaaggtcgctggacgatTTTTTaggcataggacccgtgtct 625 BP TTGAGGGGCCAGTGTCTCC 626 BP TCACAAGACAGAGGGGGGTAT 627 BP GGGGCTCCTCAAAAGGTACAG 628 BP GGTGAGGCCCCTTCAAAGTG 629 LE ggctgtgctcacttcagggtTTTTTaggcataggacccgtgtct 630 NM_002046 GAPDH BP CGGAGGGGCCATCCAC   3 LE cccacctgattttggagggaTTTTTaggcataggacccgtgtct   4 CE agcttcccgttctcagcctTTTTTctcttggaaagaaagt   5 LE ccttccacgataccaaagttgtTTTTTaggcataggacccgtgtct   6 CE ccttttggctcccccctTTTTTctcttggaaagaaagt   7 LE ccagtggactccacgacgtacTTTTTaggcataggacccgtgtct   8 CE tgacggtgccatggaatttTTTTTctcttggaaagaaagt   9 LE ggcatggactgtggtcatgagtTTTTTaggcataggacccgtgtct  10 LE gggtgctaagcagttggtggtTTTTTaggcataggacccgtgtct  11 LE agtcttctgggtggcagtgatTTTTTaggcataggacccgtgtct  12 BP AACATGGGGGCATCAGCA  13 BP CATGGTTCACACCCATGACG  14 BP gcaggaggcattgctgatga  15 LE cacagccttggcagcgcTTTTTaggcataggacccgtgtct  16 LE ccagtgagcttcccgttcaTTTTTaggcataggacccgtgtct  17 BP GAGGGGGCAGAGATGATGAC  18 LE tcttgaggctgttgtcatacttctTTTTTaggcataggacccgtgtct  19 CE catggatgaccttggccagTTTTTctcttggaaagaaagt  20 BP TGGAGAGCCCCGCGG  21 CE gctcagggatgaccttgccTTTTTctcttggaaagaaagt  22 LE ttctccatggtggtgaagacgTTTTTaggcataggacccgtgtct  23 LE ccatcacgccacagtttccTTTTTaggcataggacccgtgtct  24 LE gatgggatttccattgatgacaTTTTTaggcataggacccgtgtct  25 CE gcaaatgagccccagccTTTTTctcttggaaagaaagt  26 CE tctcgctcctggaagatggtTTTTTctcttggaaagaaagt  27 LE cagtagaggcagggatgatgttcTTTTTaggcataggacccgtgtct  28 BP TCAGCGCCAGCATCGC  29 NM_020529 NFKBIA LE ggcccagctgctgctgtatTTTTTaggcataggacccgtgtct 631 BP CTGAGCATTGACATCAGCACC 632 CE tgcgaggtgaagggcagtTTTTTcccttggaaagaaagt 633 CE gtcctctgtgaactccgtgaacTTTTTctcttggaaagaaagt 634 LE ggatagaggctaagtgtagacacgTTTTTaggcataggacccgtgtct 635 LE ctctgttgacatcagccccaTTTTTaggcataggacccgtgtct 636 LE cacttcaacaggagtgacaccagTTTTTaggcataggacccgtgtct 637 LE ccggccattacagggctcTTTTTaggcataggacccgtgtct 638 LE gtcaggattttgcaggtccacTTTTTaggcataggacccgtgtct 639 LE tgtggccattgtagttggtagcTTTTTaggcataggacccgtgtct 640 BP gccccaggtgagctggta 641 BP TCATCCTCACTCTCTGGCAGC 642 LE gacgctggcctccaaacaTTTTTaggcataggacccgtgtct 643 CE cgatgcccaggtagccatTTTTTctcttggaaagaaagt 644 CE gggagaatagccctggtaggtaaTTTTTctcttggaaagaaagt 645 BP CGGGGTGGTGCAGGACT 646 CE gccaggcagccctgctcTTTTTctcttggaaagaaagt 647 BP CAAGGACACCAAAAGCTCCA 648 BP CCGGGTGCTTGGGCG 649 CE cttcaggatggagtggaggtgTTTTTctcttggaaagaaagt 650 LE tctgactctgtgtcatagctctccTTTTTaggcataggacccgtgtct 651 LE gagtcaggactcccacgctgTTTTTaggcataggacccgtgtct 652 BP cacagtcatcatagggcagctc 653 LE atctgaaggttttctagtgtcagctTTTTTaggcataggacccgtgtct 654 LE ccctttgcactcataacgtcaTTTTTaggcataggacccgtgtct 655 NM_002502 NFKB2 BP CGAGGTGGGTCACTGTGTGTTAC 656 LE caggtccacctcgatcttggTTTTTaggcataggacccgtgtct 657 LE tactcagatccatcaccttcttcaTTTTTaggcataggacccgtgtct 658 LE ccagactgtgggcatgagcaTTTTTaggcataggacccgtgtct 659 LE cgcacagagcctgctgtcttTTTTTaggcataggacccgtgtct 660 LE gtccattcgagaaatcttcaggTTTTTaggcataggacccgtgtct 661 BP gcccttctcactggaggcac 662 LE actggctctaaggaaggcagaTTTTTaggcataggacccgtgtct 663 BP AGGGGCCTTCACAGCCAT 664 BP ctggtccctcgtagttacagatct 665 LE tgggccccacagaaacgTTTTTaggcataggacccgtgtct 666 CE atcgaaatcggaagcctctcTTTTTctcttggaaagaaagt 667 CE cctccgtaaggccctgggTTTTTctcttggaaagaaagt 668 LE tgacagtgggataggtctttcgTTTTTaggcataggacccgtgtct 669 BP gaagcgcagccgcacta 670 BP TGCCTCTGAAGTTTTTGTATCATAGT 671 BP ttgctatcatggatgggctg 672 CE gttctttggcctcttgctccTTTTTctcttggaaagaaagt 673 LE ttaaattgggcagtcatgtcctTTTTTaggcataggacccgtgtct 674 LE catgcaggacacccaggttgTTTTTaggcataggacccgtgtct 675 CE ggaggtgactggcttcagggTTTTTctcttggaaagaaagt 676 BP AGCTCCCGCTGCTCGG 677 LE gcctagagcggagccgcTTTTTaggcataggacccgtgtct 678 CE cgagcattgcttgcccaTTTTTctcttggaaagaaagt 679 LE gcagggagaaggagccatcTTTTTaggcataggacccgtgtct 680 LE gcgcagatccccagctcTTTTTaggcataggacccgtgtct 681 LE ccccatcatgttcttcttagtcaTTTTTaggcataggacccgtgtct 682 CE tttgatgcccccggagatTTTTTctcttggaaagaaagt 683 LE cgggcagtcctccatgggTTTTTaggcataggacccgtgtct 684 NM_021975 RELA BP AGGCCGAGGCCTGGC 685 LE gctgaaactcggagttgtcgaTTTTTaggcataggacccgtgtct 686 CE cgttccttccccagcctgTTTTTctcttggaaagaaagt 687 CE acgtaaagggatagggctggTTTTTctcttggaaagaaagt 688 LE ccatggtgggaaactcatcatTTTTTaggcataggacccgtgtct 689 LE gtcttcatcatcaaactgcagctTTTTTaggcataggacccgtgtct 690 BP GGTGCTGGCTTGGGGACA 691 BP GGACTGGGACAGGGGCTG 692 CE tgccctggttcagcagctTTTTTctcttggaaagaaagt 693 LE ccaagcaaggcccccagTTTTTaggcataggacccgtgtct 694 CE cggatgccaggtctgtgaacaTTTTTctcttggaaagaaagt 695 BP gataccatggctggagcagg 696 BP GGGCCTGGGCCAGAGCT 697 BP GGTGGGCTTGGGGGCA 698 BP GGTGGGGCCACAGCCTG 699 LE gaaggtctcatatgtccttttacgtTTTTTaggcataggacccgtgtct 700 LE gcgagttatagcctcagggtactcTTTTTaggcataggacccgtgtct 701 BP CAGCTGGGTCTGTGCTGTTG 702 BP ggcacagcaatgcgtcga 703 BP AGGAGGGCCTGGGGCTA 704 BP GGTGGAGGCCGGGGG 705 BP GGCAGGGGCTGGAGCCT 706 BP GGGGCAGGACTTGGGGA 707 CE aggactcttcttcatgatgctcttTTTTTctcttggaaagaaagt 708 CE tgatctgcccagaaggaaacaTTTTTctcttggaaagaaagt 709 BP gcagcagggcctctgacag 710 LE ttctcctcaatccggtgacgTTTTTaggcataggacccgtgtct 711 LE ggcctctgggctgtcactagTTTTTaggcataggacccgtgtct 712 BP GTGGGGGGCCACAGGTA 713 BP GAAGCTGAGCTGCGGGAA 714 BP catcagcatgggctcagttgt 715 BP GGGGCCGGGGCCA 716 LE agttgatggtgctcagggatgTTTTTaggcataggacccgtgtct 717 LE tcggtgggtccgctgaaTTTTTaggcataggacccgtgtct 718 NM_003998 NFKB1 CE ccaggattatagccccttatacaTTTTTctcttggaaagaaagt 719 BP TGTCACATGAAGTATACCCAGGTTT 720 BP TCTGGATTAAATATTGTATGAGTCAAAG 721 LE gcgaagccgaccaccatTTTTTaggcataggacccgtgtct 722 LE tttccatttgtgaccaactgaaTTTTTaggcataggacccgtgtct 723 CE tcaggccttcccaaatatggTTTTTctcttggaaagaaagt 724 LE catagttgcagattttgacctgagTTTTTaggcataggacccgtgtct 725 LE ctgcttggcggattagctcTTTTTaggcataggacccgtgtct 726 CE ggttgctctaatatttgaaggtatgTTTTTctcttggaaagaaagt 727 LE aaggatccaaatgaaacatttgtTTTTTaggcataggacccgtgtct 728 LE ggccatctgctgttggcaTTTTTaggcataggacccgtgtct 729 LE gtgttttcccaccaggctgtTTTTTaggcataggacccgtgtct 730 LE ggtaagacttcttgttcttttcactagaTTTTTaggcataggacccgtgtct 731 LE gtgccatctgtggttgaaatactTTTTTaggcataggacccgtgtct 732 BP GGATGGGCCTTCACATACATAAC 733 LE ggcaccaggtagtccaccatgTTTTTaggcataggacccgtgtct 734 BP AGTGCAGATCCCATCCTCACA 735 CE tttttcccgatctcccagcTTTTTctcttggaaagaaagt 736 BP TCCAGTGTTTCAAATACTTTTTTCTT 737 BP GGAAACGAAATCCTCTCTGTTTA 738 CE gggcatgcaggtggatatttTTTTTctcttggaaagaaagt 739 LE cttctgcttgcaaataggcaaTTTTTaggcataggacccgtgtct 740 LE ggtcagggtgcaccaagagtTTTTTaggcataggacccgtgtct 741 LE cgcctctgtcattcgtgctTTTTTaggcataggacccgtgtct 742 CE gtccttgggtccagcagttacTTTTTctcttggaaagaaagt 743 BP TGCCGGTCCCCTCCAC 744 LE caataacctttgctggtcccaTTTTTaggcataggacccgtgtct 745 NM_006290 TNFAIP3 BP ggcgtcgtttccagctctg 746 CE gggccttgaggtgctttgTTTTTctcttggaaagaaagt 747 LE gatgctgacactccatgcagaTTTTTaggcataggacccgtgtct 748 BP GCGCTGGCTCGATCTCAGTT 749 LE gtgggactgactttccctgagTTTTTaggcataggacccgtgtct 750 BP GAGTCCCAAAATACACGCAGC 751 LE cgtccccgtcctgtcccTTTTTaggcataggacccgtgtct 752 CE cgcgagggatctgacttggaTTTTTctcttggaaagaaagt 753 BP GGCCCGGGCGCACTT 754 BP TGCAAAAGCCCTTGTTTTCTG 755 LE gccaggatgttcttgcaggaTTTTTaggcataggacccgtgtct 756 LE acgctggtgacaggaagaagTTTTTaggcataggacccgtgtct 757 LE caatgaaacacttctggcagtatcTTTTTaggcataggacccgtgtct 758 CE catgaaatctctgattctgagcttTTTTTctcttggaaagaaagt 759 LE ggaggctggtgctgaggcTTTTTaggcataggacccgtgtct 760 CE gctcctcgctgcggcagTTTTTctcttggaaagaaagt 761 CE cggcttttctgcacttgctTTTTTctcttggaaagaaagt 762 BP TGGAGGAGGCCTCTGCTGT 763 LE agatcccattaaatgtcctggtaTTTTTaggcataggacccgtgtct 764 LE tgttctggaacctggacgctTTTTTaggcataggacccgtgtct 765 BP TCTCTGTACTCGATGAAACACAGTG 766 LE tgtggttcgaggcacatctctTTTTTaggcataggacccgtgtct 767 BP TGGCAAGAATGCGGGGA 768 BP GCAGCAGCAAAATGTTTGTTT 769 LE agtccttttgaagcaagtactgcTTTTTaggcataggacccgtgtct 770 BP CAGGAGTCCGTGCAGCTTG 771 LE cttcaaacatggtgcttccaaTTTTTaggcataggacccgtgtct 772 LE gctcttctgtccttttggcctTTTTTaggcataggacccgtgtct 773 BP agacaggcagccagcagg 774 BP GGGGCTCCGGACGAGC 775 CE ccccaggcacggaatggTTTTTctcttggaaagaaagt 776 BP GGGTGCCGCATTCCCT 777 NM_000600 IL6 BP TCTAGGTATACCTCAAACTCCAAAAG 778 LE atgtaccgaatttgtttgtcaattTTTTTaggcataggacccgtgtct 779 CE cgttctgaagaggtgagtggctTTTTTctcttggaaagaaagt 780 LE caagtctcctcattgaatccagatTTTTTaggcataggacccgtgtct 781 LE aacaacataagttctgtgcccagTTTTTaggcataggacccgtgtct 782 BP CCATCTTTGGAAGGTTCAGGT 783 CE cctttttctgcaggaactggatTTTTTctcttggaaagaaagt 784 LE catctttggaatcttctcctggTTTTTaggcataggacccgtgtct 785 LE caggacttttgtactcatctgcacTTTTTaggcataggacccgtgtct 786 LE ttgttacatgtctcctttctcaggTTTTTaggcataggacccgtgtct 787 CE gctgagatgccgtcgaggTTTTTctcttggaaagaaagt 788 BP TGCTGCTTTCACACATGTTACTC 789 LE tggaagcatccatctttttcagTTTTTaggcataggacccgtgtct 790 CE ccttaaagctgcgcagaatgTTTTTctcttggaaagaaagt 791 BP GGGTACTGGGGCAGGGAA 792 BP GTCTGTGTGGGGCGGCTA 793 BP ccactggttctgtgcctgca 794 LE agatgagttgtcatgtcctgcagTTTTTaggcataggacccgtgtct 795 LE accagtgatgattttcaccaggTTTTTaggcataggacccgtgtct 796 LE ggcagcaggcaacaccagTTTTTaggcataggacccgtgtct 797 LE acatttgccgaagagccctTTTTTaggcataggacccgtgtct 798 LE catttgtggttgggtcagggTTTTTaggcataggacccgtgtct 799 BP AAGGAATGCCCATTAACAACAA 800 LE tggacaggtttctgaccagaagTTTTTaggcataggacccgtgtct 801 LE tgttttctgccagtgcctcttTTTTTaggcataggacccgtgtct 802 LE actctcaaatctgttctggaggtacTTTTTaggcataggacccgtgtct 803 LE agctctggcttgttcctcactTTTTTaggcataggacccgtgtct 804 CE cgctcatacttttagttctccatagagTTTTTctcttggaaagaaagt 805 CE caatctgaggtgcccatgdtTTTTTctcttggaaagaaagt 806 LE caggctggactgcaggaactTTTTTaggcataggacccgtgtct 807 LE gtggttattgcatctagattctttgTTTTTaggcataggacccgtgtct 808 BP gcttcgtcagcaggctgg 809 NM_000594 TNF CE cgagaagatgatctgactgcctgTTTTTctcttggaaagaaagt 810 LE cagaagaggttgagggtgtctgaTTTTTaggcataggacccgtgtct 811 LE gcggctgatggtgtgggTTTTTaggcataggacccgtgtct 812 LE aggtacaggccctctgatggTTTTTaggcataggacccgtgtct 813 CE gctgcccctcagcttgagTTTTTctcttggaaagaaagt 814 CE tcgggccgattgatctcaTTTTTctcttggaaagaaagt 815 LE ggcggttcagccactggaTTTTTaggcataggacccgtgtct 816 BP AGGCTTGTCACTCGGGGTT 817 BP tctccagctggaagacccc 818 BP caccaccagctggttatctctc 819 LE ggccagagggctgattagagaTTTTTaggcataggacccgtgtct 820 BP AGGAGGGGGTAATAAAGGGAT 821 LE ggtttgctacaacatgggctacTTTTTaggcataggacccgtgtct 822 LE agactcggcaaagtcgagatagTTTTTaggcataggacccgtgtct 823 CE cccccaattctctttttgagcTTTTTctcttggaaagaaagt 824 BP TGGCAGGGGCTCTTGATG 825 CE gtctggtaggagacggcgatTTTTTctcttggaaagaaagt 826 LE gcttgggttccgaccctaagTTTTTaggcataggacccgtgtct 827 BP TGGGGCAGGGGAGGC 828 BP GTTTGGGAAGGTTGGATGTTC 829 LE atcccaaagtagacctgcccTTTTTaggcataggacccgtgtct 830 BP CCCCTCTGGGGTCTCCCTC 831 LE caggagggcattggcccTTTTTaggcataggacccgtgtct 832 LE gcagagaggaggttgaccttgTTTTTaggcataggacccgtgtct 833 LE gtcctcctcacagggcaatgTTTTTaggcataggacccgtgtct 834 CE tcccagatagatgggctcatacTTTTTctcttggaaagaaagt 835 LE cagggcttggcctcagcTTTTTaggcataggacccgtgtct 836 LE tgaggagcacatgggtggagTTTTTaggcataggacccgtgtct 837 BP tgaagaggacctgggagtagatg 838 BP GCGCTGAGTCGGTCACCCT 839 LE agctccacgccattggcTTTTTaggcataggacccgtgtct 840 BP GGGCAGCCTTGGCCCT 841

While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be clear to one skilled in the art from a reading of this disclosure that various changes in form and detail can be made without departing from the true scope of the invention. For example, all the techniques and apparatus described above can be used in various combinations. All publications, patents, patent applications, and/or other documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent, patent application, and/or other document were individually indicated to be incorporated by reference for all purposes. 

1-25. (canceled)
 26. A composition comprising: a first set of n capture extenders, wherein n is at least two, which first set of capture extenders is capable of hybridizing to a first target nucleic acid; a solid support, wherein a first capture probe is bound to the solid support, the first capture probe being capable of hybridizing to the capture extenders of the first set and thereby associating the capture extenders with the solid support; a whole blood lysate, which whole blood lysate comprises peripheral blood cell nucleic acids and the first target nucleic acid; and an exogenously supplied protease; wherein the first target nucleic acid is hybridized to the first set of capture extenders, which capture extenders are hybridized to the first capture probe, whereby the first target nucleic acid is associated with the solid support; wherein the composition is maintained at a hybridization temperature which is greater than a melting temperature (T_(m)) of a complex between each individual capture extender and the capture probe. 27-28. (canceled)
 29. The composition of claim 26, wherein the peripheral blood cell nucleic acids comprise the first target nucleic acid.
 30. The composition of claim 26, wherein the first target nucleic acid is an RNA.
 31. The composition of claim 26, wherein the first target nucleic acid is a DNA.
 32. (canceled)
 33. The composition of claim 26, wherein n is at least three.
 34. The composition of claim 26, wherein n is at most
 10. 35-36. (canceled)
 37. The composition of claim 26, wherein the solid support is a substantially planar solid support.
 38. The composition of claim 26, wherein the solid support comprises a plurality of particles.
 39. The composition of claim 26, comprising a second set of m capture extenders, wherein m is at least two, which second set of capture extenders is capable of hybridizing to a second target nucleic acid, wherein a second capture probe is bound to the solid support, the second capture probe being capable of hybridizing to the capture extenders of the second set and thereby associating the capture extenders with the solid support.
 40. The composition of claim 39, comprising the second target nucleic acid.
 41. The composition of claim 39, wherein the solid support is a substantially planar solid support, wherein the first capture probe is predisposed at a first selected position on the solid support, whereby the first set of capture extenders is associated with the first selected position on the solid support, and wherein the second capture probe is predisposed at a second selected position on the solid support, whereby the second set of capture extenders is associated with the second selected position on the solid support.
 42. The composition of claim 39, wherein the solid support comprises a population of particles, the population comprising at least two sets of particles, the particles in each set being distinguishable from the particles in every other set; wherein a first set of particles comprises the first capture probe, whereby the first set of capture extenders is associated with the first set of particles; and wherein a second set of particles comprises the second capture probe, whereby the second set of capture extenders is associated with the second set of particles.
 43. (canceled)
 44. The composition of claim 26, comprising a first set of one or more label extenders, which first set of label extenders is capable of hybridizing to the first target nucleic acid, and/or a label probe system comprising a label.
 45. The composition of claim 44, wherein the label probe system comprises an amplification multimer and a plurality of label probes, wherein the amplification multimer is capable of hybridizing simultaneously to a label extender and to a plurality of label probes.
 46. The composition of claim 45, wherein the label probe comprises the label.
 47. The composition of claim 44, wherein the label is a fluorescent label or an enzyme. 48-69. (canceled)
 70. The composition of claim 39, comprising five or more sets of at least two capture extenders, each of which sets is capable of hybridizing to one of five or more target nucleic acids; wherein the solid support comprises five or more capture probes bound to the solid support.
 71. The composition of claim 26, wherein the exogenously supplied protease is proteinase K.
 72. The composition of claim 71, wherein the proteinase K is at a concentration of at least 1 mg per ml of the whole blood lysate.
 73. The composition of claim 26, wherein the volume of whole blood from which the whole blood lysate is produced is at most ⅕ the volume of the composition. 